This Rmarkdown notebook describes the analysis of bulkRNAseq data of Amphiprion ocellaris larvae treated with a selection of drugs from 8dph to 13dph (5 days total), i.e. until control larvae had metamorphosed. The aim of the experiment was to detect the general effects of the organophosphate pesticide Chlorpyrifos (CPF) on clownfish larvae as they undergo metamorphosis, and specifically on their thyroid hormone signalling pathway. n=10 larvae were collected at the end of each of the 5 treatments (i.e. at 13dph), RNA was extracted from each larva, and RNA was sequenced (total n=50). Treatments: DMSO (control), T3+IOP (positive control, induction of metamorphosis), MPI (negative control, blockade of metamorphosis), CPF (test drug), CPF+T3+IOP.
Step 1: We start by creating a data-table
summarising sample metadata
Step 2: we will take the chance here to create
another quality control step: the number or reads processed and the
number + percentage of those reads that could be mapped by salmon.
[1] "Expected number of total reads/lane (P3cell): 14 millions"
[1] "Median number of total reads/lane: 11.97 millions"
[1] "Median number of mapped reads/lane: 10.19 millions"
[1] "Average mapping percentage/lane: 85.12 %"
Step 3: Transcripts need to be associated with
gene IDs for gene-level summarization. For Salmon, Sailfish, and
kallisto the files only provide the transcript ID. We first make a
data.frame called tx2gene with two columns: 1) transcript ID and 2) gene
ID. The column names do not matter but this column order must be used.
The transcript ID must be the same one used in the abundance files.
Import genomic features from the file as a GRanges object ... OK
Prepare the 'metadata' data frame ... OK
Make the TxDb object ... Warning: some transcripts have no "transcript_id" attribute ==> their name ("tx_name"
column in the TxDb object) was set to NAWarning: the transcript names ("tx_name" column in the TxDb object) imported from the
"transcript_id" attribute are not uniqueOK
[1] "CDSCHROM" "CDSEND" "CDSID" "CDSNAME" "CDSPHASE" "CDSSTART"
[7] "CDSSTRAND" "EXONCHROM" "EXONEND" "EXONID" "EXONNAME" "EXONRANK"
[13] "EXONSTART" "EXONSTRAND" "GENEID" "TXCHROM" "TXEND" "TXID"
[19] "TXNAME" "TXSTART" "TXSTRAND" "TXTYPE"
'select()' returned 1:1 mapping between keys and columns
Salmon output transcript-based quantification files (quant.sf) are imported in RStudio and summarised at the gene level using the tximport function from the tximport package (RRID:SCR_016752; Soneson et al., 2015), referencing the gene models of Amphiprion ocellaris reference genome assembly ASM2253959v1. The counts matrix is obtained by re-calculating counts through the flag countsFromAbundance = “lengthScaledTPM”.
reading in files with read_tsv
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100
summarizing abundance
summarizing counts
summarizing length
Giving the following count matrix (first rows only, shown here)
DMSO_1_L001 DMSO_1_L002 DMSO_2_L001 DMSO_2_L002 DMSO_3_L001 DMSO_3_L002
111562382 174.49927 155.01513 243.44150 236.60197 229.67726 213.4546
111562384 85.27148 67.18561 104.56237 106.52691 96.54412 120.8456
111562387 344.31048 324.44902 455.45251 449.47389 390.32455 354.2029
111562388 109.66176 113.74703 158.98551 156.87357 137.87634 146.7163
111562389 115.95570 119.07018 83.45771 76.24195 115.49280 117.4767
111562390 615.82549 498.81599 643.18265 623.10037 614.13545 496.1659
DMSO_4_L001 DMSO_4_L002 DMSO_5_L001 DMSO_5_L002 DMSO_6_L001 DMSO_6_L002
111562382 179.15656 155.77403 184.40274 202.63497 195.10835 194.9388
111562384 62.48445 66.76861 85.14152 62.26721 89.03561 106.0413
111562387 274.46198 296.92529 358.87272 343.94857 392.83484 388.9179
111562388 97.07839 115.01655 111.59803 101.90645 153.35882 110.7220
111562389 102.56266 104.83907 126.85109 125.82110 124.33455 123.4520
111562390 511.18928 451.28487 582.24478 563.96261 624.85964 622.1594
DMSO_7_L001 DMSO_7_L002 DMSO_8_L001 DMSO_8_L002 DMSO_9_L001 DMSO_9_L002
111562382 167.25224 149.36060 214.1726 198.28576 190.1222 178.77244
111562384 74.53525 71.04665 109.4157 68.00025 105.6287 85.22376
111562387 477.23735 422.17716 422.1399 374.03702 359.6164 343.10091
111562388 115.47017 112.89865 111.2855 125.98404 124.8813 117.71145
111562389 102.45378 89.71627 137.7581 115.06824 134.5694 109.72243
111562390 671.16469 628.24405 618.3855 533.81812 634.0491 587.44159
DMSO_10_L001 DMSO_10_L002 T3IOP_1_L001 T3IOP_1_L002 T3IOP_2_L001 T3IOP_2_L002
111562382 261.03752 212.65119 245.3586 216.29409 344.4239 329.3328
111562384 90.75693 97.95856 119.7603 108.05098 121.8247 107.8747
111562387 330.65116 331.26688 483.9010 441.66918 515.8391 470.2383
111562388 145.79954 127.02024 101.3422 86.97984 148.9324 149.4578
111562389 121.50721 148.75099 141.4935 126.84049 130.2880 112.3220
111562390 563.75717 563.54146 624.0920 560.01498 618.1341 579.2623
T3IOP_3_L001 T3IOP_3_L002 T3IOP_4_L001 T3IOP_4_L002 T3IOP_5_L001 T3IOP_5_L002
111562382 222.89618 232.37461 233.71160 265.58786 279.94761 296.71854
111562384 78.00563 86.99129 95.81763 77.86007 98.15427 96.10638
111562387 365.92370 329.36678 370.90553 385.91696 297.17730 325.76390
111562388 112.33992 89.41192 131.67561 101.84649 127.72516 91.41058
111562389 115.30082 105.11769 110.90219 123.88338 103.02913 104.12463
111562390 428.26314 442.19840 495.76038 433.81402 409.98397 381.99520
T3IOP_6_L001 T3IOP_6_L002 T3IOP_7_L001 T3IOP_7_L002 T3IOP_8_L001 T3IOP_8_L002
111562382 274.29383 279.1833 240.24271 265.18012 207.48094 211.20141
111562384 89.13959 119.9247 97.32910 88.29723 78.28923 97.46790
111562387 385.04857 362.5347 359.07718 319.97562 471.34108 425.87513
111562388 117.08165 125.7437 96.17673 94.60925 121.52339 86.21991
111562389 123.97308 136.4261 117.48356 91.62023 96.41757 90.22210
111562390 479.88948 517.3039 470.81316 397.12914 613.38273 522.95053
T3IOP_9_L001 T3IOP_9_L002 T3IOP_10_L001 T3IOP_10_L002 MPI_1_L001 MPI_1_L002
111562382 270.2915 229.00931 297.7791 288.71756 180.11282 163.04481
111562384 102.6530 83.23698 108.0160 99.47370 89.02595 76.46529
111562387 408.1966 398.36347 427.3041 336.27062 216.14249 252.71947
111562388 133.7920 117.12194 149.5709 115.85962 110.25600 95.81815
111562389 111.7951 123.05926 104.5029 84.86838 125.78927 110.82192
111562390 633.6103 551.98987 399.8288 423.91686 486.05008 435.89843
MPI_2_L001 MPI_2_L002 MPI_3_L001 MPI_3_L002 MPI_4_L001 MPI_4_L002 MPI_5_L001
111562382 189.7147 132.15352 205.66363 200.9395 235.6264 257.9170 224.9165
111562384 106.5600 83.33481 87.33034 100.0202 186.4960 157.4411 113.3053
111562387 307.9446 282.29500 382.63849 351.8394 493.6531 474.1928 435.6347
111562388 133.1730 93.43760 131.66876 119.8062 185.3451 130.5302 128.5497
111562389 123.1416 105.21880 122.94080 103.6464 151.0294 136.3279 113.2497
111562390 515.0996 439.71438 524.92603 479.4113 769.9098 642.3746 609.5665
MPI_5_L002 MPI_6_L001 MPI_6_L002 MPI_7_L001 MPI_7_L002 MPI_8_L001 MPI_8_L002
111562382 210.22161 263.1316 271.16831 128.7042 118.58025 245.7517 175.77239
111562384 67.63475 169.1850 159.81788 125.4149 114.80072 101.2239 92.40544
111562387 402.38737 334.1766 283.31321 298.9213 329.30282 339.8667 263.56397
111562388 128.27394 147.8648 117.72585 131.5252 100.76532 117.8058 108.22243
111562389 110.69764 119.3306 97.02815 148.7625 96.50586 113.4863 112.00050
111562390 586.06219 516.4724 468.79087 486.8263 505.73047 471.1170 478.12951
MPI_9_L001 MPI_9_L002 MPI_10_L001 MPI_10_L002 CPF_1_L001 CPF_1_L002 CPF_2_L001
111562382 315.9798 263.53210 340.93646 286.90998 314.68698 310.7790 268.8759
111562384 127.6321 75.37440 86.81161 85.41433 206.38214 176.4612 147.2713
111562387 358.8427 347.67937 481.23499 393.80918 424.49127 378.0380 522.9490
111562388 170.1223 135.64507 136.81824 119.48236 186.78947 179.2926 167.2089
111562389 123.4830 98.41378 111.58102 115.51053 85.69544 105.4417 125.0696
111562390 589.7763 547.11062 591.02914 582.65329 563.13010 450.8035 618.2207
CPF_2_L002 CPF_3_L001 CPF_3_L002 CPF_4_L001 CPF_4_L002 CPF_5_L001 CPF_5_L002
111562382 210.03618 264.5331 255.4583 272.2664 279.4593 360.24938 333.1920
111562384 138.18565 101.8031 116.0798 150.8250 111.0829 176.06080 164.2611
111562387 459.96073 395.9295 347.0004 359.0079 312.9936 328.06958 303.5440
111562388 194.81672 144.3295 157.7885 138.6746 147.9768 254.68317 219.6172
111562389 89.71017 103.7674 106.7122 127.0001 111.0298 91.55575 94.0644
111562390 596.58965 497.1387 464.4037 520.0877 440.2759 496.07779 415.9939
CPF_6_L001 CPF_6_L002 CPF_7_L001 CPF_7_L002 CPF_8_L001 CPF_8_L002 CPF_9_L001
111562382 301.7989 307.3282 265.5805 203.2814 242.5027 195.3063 183.3371
111562384 189.7308 155.4377 126.7522 119.5535 162.4235 138.2780 131.0619
111562387 342.0361 322.1199 474.4700 499.1928 413.7643 364.6644 373.1001
111562388 209.9633 174.0434 191.9434 193.6604 160.1680 157.8631 164.3745
111562389 96.5134 84.1090 142.1541 147.9641 117.9591 151.7439 126.2157
111562390 527.8405 433.9670 722.8828 649.8957 646.2303 596.4632 564.3842
CPF_9_L002 CPF_10_L001 CPF_10_L002 CPF.T3IOP_1_L001 CPF.T3IOP_1_L002
111562382 190.39182 250.7338 225.2428 294.0099 246.0184
111562384 99.04989 119.9420 111.7895 117.7968 107.9069
111562387 341.74475 285.0139 279.4609 552.0897 511.8303
111562388 126.70850 164.8267 160.2755 161.3292 125.7272
111562389 116.37144 106.5926 118.1142 124.6086 137.3307
111562390 539.72880 325.9654 338.8546 547.9507 518.7638
CPF.T3IOP_2_L001 CPF.T3IOP_2_L002 CPF.T3IOP_3_L001 CPF.T3IOP_3_L002
111562382 243.5936 247.0799 310.94402 266.70747
111562384 147.0141 158.6848 105.40969 126.35028
111562387 537.8212 448.2016 389.97434 357.37107
111562388 128.5554 120.2410 149.94394 139.31410
111562389 124.3283 136.1966 90.96512 86.52713
111562390 635.1143 601.9102 446.04206 370.86341
CPF.T3IOP_4_L001 CPF.T3IOP_4_L002 CPF.T3IOP_5_L001 CPF.T3IOP_5_L002
111562382 336.1650 341.66850 231.7827 251.9496
111562384 147.6791 131.25056 119.9850 111.9610
111562387 332.1079 264.65628 381.4214 360.0748
111562388 173.3817 152.23589 151.4143 137.5173
111562389 98.8082 84.20097 152.4719 117.0637
111562390 397.2637 378.39184 609.7407 625.0679
CPF.T3IOP_6_L001 CPF.T3IOP_6_L002 CPF.T3IOP_7_L001 CPF.T3IOP_7_L002
111562382 228.5020 242.9268 254.5090 258.14442
111562384 121.6659 136.4584 129.4447 122.64942
111562387 476.4058 463.1779 447.9883 440.60226
111562388 161.8704 138.7580 140.0269 141.77364
111562389 126.8840 139.4097 105.8712 98.13592
111562390 835.6492 738.4252 615.5554 618.13991
CPF.T3IOP_8_L001 CPF.T3IOP_8_L002 CPF.T3IOP_9_L001 CPF.T3IOP_9_L002
111562382 232.7558 185.5054 286.0427 240.1374
111562384 126.8146 130.3076 147.9219 120.2160
111562387 475.6336 387.3153 410.9325 357.2355
111562388 149.5676 140.4665 149.7141 163.8598
111562389 115.7287 120.7027 147.4524 120.3669
111562390 650.3048 568.4508 596.0250 611.7181
CPF.T3IOP_10_L001 CPF.T3IOP_10_L002
111562382 244.9702 218.98506
111562384 147.0980 133.72432
111562387 335.2116 289.98481
111562388 134.4904 93.35917
111562389 107.3636 94.01700
111562390 496.3520 468.82866
Step 1: We first collect the file with the
sample metadata (as created earlier)
Step 2: We then collect the counts matrix as
imported from Salmon with tximport
Step 3: Now, we can create a DGEList object.
This is an object used by edgeR to store count data. It has a number of
slots for storing various parameters about the data.
Step 4: We then collect the last missing piece
of information, the gene metadata info (in this case, it is loaded from
a custom-curated reference file based on the integration of Ensembl
(still based on assembly AmpOce1.0) and NCBI annotations )
we loaded this information too into the DGE_list object, after
manual annotation of some genes, and filling in of missing values.
[1] 26889
Mode FALSE TRUE
logical 2241 26889
How is count data distributed? not normally, as shown by the plot below. Moreover, the variance is bigger than the mean, meaning that a negative binomial, rather than a poisson, describes count data.
Count data is not normally distributed, so if we want to examine the distributions of the raw counts we need to log the counts. Next we’ll use box plots to check the distribution of the read counts on the log2 scale. We can use the cpm function to get log2 counts per million, which are corrected for the different library sizes. The cpm function also adds a small offset (0.25) to avoid taking log of zero.
Below, a comparison between gene counts before and after log
transformation and Counts per Million (to account for different library
sizes). The distribution of the counts is shown as a density plot bottom
right. Control, T3 , MPI
, CPF , CPF+T3.
You should filter with CPMs rather than filtering on the counts directly, as the latter does not account for differences in library sizes between samples.
Set a CPM threshold that corresponds to a count of 10-15 for the library sizes in your data set (e.g. 0.5 for a library of around 20million). 0.5 COUNTS PER MILLION * 20millions = 10 COUNTS. If the count is any smaller, it is considered to be very low, indicating that the associated gene is not expressed in that sample.
A requirement for expression in 10 or more libraries is used as each group contains 10 replicates. This ensures that a gene will be retained if it is only expressed in one group. Smaller CPM thresholds are usually appropriate for larger libraries. As a general rule, a good threshold can be chosen by identifying the CPM that corresponds to a count of 10.
What counts as “lowly expressed” depends on library size. We will now find library sizes of each sample. First, we can check how many reads we have for each sample in the DGE object (this is automatic calculated by the DGE object).
The max library size is 12491570 : sample 73 : CPF_7_L001
The mean library size is 10260747
The min library size is 8154673 : sample 86 : CPF.T3IOP_3_L002
The filtering threshold of 1.226291 has been chosen
## Now that we are satisfied with CPM threshold, we can filter the data
# Find CPM values that are greater than the threshold established above
above_threshold <- counts_CPMraw > filtering_threshold
# This produces a logical matrix with TRUEs and FALSEs
# we would like to keep genes that have at least 2 TRUES in each row of "above_threshold"
keep <- rowSums(above_threshold) >= 10 # 10 because we have 10 biological replicates per condition (each with 2 lanes)
summary(keep)
Mode FALSE TRUE
logical 5351 21538
TMM normalization is performed to eliminate composition biases between libraries (Mark D. Robinson and Oshlack 2010). This generates a set of normalization factors, where the product of these factors and the library sizes defines the effective library size. The calcNormFactors function calculates the normalization factors between libraries. TMM normalisation (and most scaling normalisation methods) scale relative to one sample.
The normalization factors multiply to unity across all libraries. A normalization factor below one indicates that the library size will be scaled down, as there is more suppression (i.e., composition bias) in that library relative to the other libraries. This is also equivalent to scaling the counts upwards in that sample. Conversely, a factor above one scales up the library size and is equivalent to downscaling the counts.
Plotting mean-difference plots of the samples with biggest and with smallest normalisation factors, we should be able to see the composition bias problem. We will use the logcounts, which have been normalised for library size, but not for composition bias.
The mean-difference plots show average expression (mean: x-axis) against log-fold-changes (difference: y-axis). If we redo these plots using the TMM-normalised counts (normalisation factors are stored in the DGE object), we should see the composition bias problem has been solved.
In the sample with biggest norm.factor ( CPF.T3IOP_6_L002 ) the median expression ratio compared to other samples went from 1.050764 to 0.9746659 after TMM normalisation
In the sample with smallest norm.factor ( DMSO_4_L002 ) the median expression ratio compared to other samples went from 0.8131295 to 0.9888561 after TMM normalisation
DESeq2 internally corrects counts for sequencing depth (i.e. what we did by using CPM) and RNA compositional bias (norm) using Median of ratios method. To run this method, we create a DESeq2 object using the count data and metadata.
converting counts to integer mode
For the purpose of exploratory analysis such as MDS, PCA, clustering etc, VST (variance-stabilizing-transformation) is recommended. VST is also run using DESeq2. As in the previous step, a DESeq2 object is created. Variance stabilizing transformation (VST) aims at generating a matrix of values for which variance is constant across the range of mean values, especially for low mean.The vst function computes the fitted dispersion-mean relation, derives the transformation to apply and accounts for library size.
For RNA-seq data, as the mean count value increases, the variance increases. There is a strong almost linear relationship as seen in the figures. The statistical methods such as PCA expects similar variance across the range of mean values. If not, the higher variance genes will contribute more than the lower variance genes. Such data is said to be heteroscedastic and needs to be corrected. Correction using log transformation (with pseudocount) gives inflates the contribution of the low variance genes. To obtain similar variance across the whole range of mean values, DESeq2 offers two methods VST (variance stabilising transformation) and RLOG (regularised log transformation).
As the name suggests, VST transformation stabilizes variance across the whole range of count values. VST is recommended for clustering or visualisation. It is not intended for differential gene expression. If the size factors vary dramatically between samples, then RLOG transformation is recommended.
Below, an overview of the main dataset properties
across objects
gene-wise dispersion estimates
mean-dispersion relationship
final dispersion estimates
Overview analysis of the dataset (top variable genes)
🔎 To get a first impression of the dataset, we will calculate exploratory PCAs on all most variable genes in the dataset, regardless of the biological processes in which they are involved. What genes separate A. ocellaris larvae across the dataset?
* Step 1: For PCA and visualisation, we will
use the VST transformed object (DeSeq2 object with Variance Stabilising
Transformation applied, see previous section): Below, an overview of the
main count features of this starting object
* Step 2a: We now can subset our counts
matrix, to just keep the most variable genes. This threshold could be
chosen arbitrarily based either on number of genes (i.e. the top2000
most variable genes), or on variance of these genes (i.e. the genes with
top 10% variance). Different possible thresholds on this dataset are
illustrated below:
* Step 2b: Here, we will select based on a
variance threshold, but not an aribitrary one. We wukk select the genes
with higest variance, based on the inflection point of the variance
distribution of all genes. As per below:
[1] "The sample variance cutoff of s^2>0.21 has been selected based on the kneedle algorithm"
[1] "There are 3418 genes whose variance across all samples is above this threshold (15.87% of all genes)"
* Step 3: We can now subset our object. In
this case, we are thus using 3418 genes, the most variable ones. The
plots below show the summary properties of this subset (note indeed the
high variance). In blue in the mean-variance plot 🔹, the genes that
have been selected out of all of the genes in the original object.
We can run the PCA based on the top variable genes. Below, the scree plot indicating the contribution of each Principal Component, and the plot of the PCA over the top10 components.
* Step 2: The scree plot shows that most of
the variance present in the dataset can be represented in two
dimensions. Below is the PC1 vs PC2 summary plot, coloured by condition,
with and without labels to correlate points to the actual larval samples
(of which we have pictures)
* Step 3: With added polygons to highlight
the spread of samples within each condition (this is the final figure
reported in the paper)
We will here analyse the main genes driving separation along PC1.
Below, the biplot showing the relative influence of each of the genes
Below, a dedicated visualisation of the relative level of
expression of each gene, in each sample.
We will here analyse the main genes driving separation along PC2.
Below, a dedicated visualisation of the relative level of
expression of each gene, in each sample.
Explore sample distribution PC2 drivers
We will here analyse the main genes driving separation along PC3.
Below, the relative expression level
Explore sample distribution PC3 drivers
We will here analyse the main genes driving separation along PC4.
Below, the relative expression level of each gene
We will here analyse the main genes driving separation along PC5.
Below, the relative expression level of each gene:
We will here analyse the main genes driving separation along PC6
Below, the relative expression level of each gene:
🔎 An alternative to PCA for examining relationships between samples is using hierarchical clustering. Heatmaps are a nice visualisation to examine hierarchical clustering of samples.
| entrez_ID | description |
|---|---|
| 111583913 | iodothyronine deiodinase 1 |
| 111563633 | iodothyronine deiodinase 2 |
| 111586185 | iodothyronine deiodinase 3a |
| 111573799 | thyroxine 5-deiodinase-like |
| 111588109 | thyroglobulin |
| 111577711 | dual oxidase |
| 111577709 | dual oxidase 2 |
| 111576557 | solute carrier family 5 member 5 |
| 111565036 | selenocysteine lyase |
| 111562581 | thyroid peroxidase |
| 111585831 | solute carrier family 16 member 10 |
| 111580672 | solute carrier organic anion transporter family member 1C1-like.1 |
| 111581275 | solute carrier family 3 member 2a |
| 111572371 | solute carrier family 7 member 11 |
| 111575976 | thyroid hormone receptor alpha.1 |
| 111566418 | thyroid hormone receptor alpha |
| 111573399 | thyroid hormone receptor beta |
| 111568343 | nuclear receptor subfamily 1, group H, member 4 |
| 111588196 | hepatic sodium/bile acid cotransporter-like |
| 111569563 | solute carrier family 10 member 1 |
| 111565180 | hematopoietically expressed homeobox |
| 111570790 | Kruppel-like factor 9 |
| 118470383 | NK2 homeobox 1.1 |
| 111573897 | paired box 2a |
| 111567846 | paired box protein Pax-2a-like |
| 111567309 | paired box 8 |
| 111566720 | mediator complex subunit 1 |
| 111565463 | nuclear receptor coactivator 1 |
| 111587689 | nuclear receptor coactivator 2 |
| 111579940 | nuclear receptor coactivator 3-like.1 |
| 111575203 | nuclear receptor corepressor 1 |
| 111581903 | nuclear receptor corepressor 2 |
| 111571366 | solute carrier family 16 member 2 |
| 111576582 | solute carrier family 2, facilitated glucose transporter member 1-like.1 |
| 111580035 | solute carrier family 2 member 1b |
| entrez_ID | description |
|---|---|
| 111575142 | corticotropin releasing hormone binding protein.1 |
| 111584834 | thyrotropin-releasing hormone receptor a |
| 111568983 | thyrotropin-releasing hormone receptor b |
| 111571736 | thyrotropin-releasing hormone-degrading ectoenzyme-like.1 |
| entrez_ID | description |
|---|---|
| 111575142 | corticotropin releasing hormone binding protein.1 |
| 111584347 | corticotropin-releasing factor receptor 1 |
| 111580118 | pro-opiomelanocortin |
| 111577563 | proopiomelanocortin a |
| 111584656 | pro-opiomelanocortin.1 |
| 111571458 | urocortin 3, like |
| entrez_ID | description |
|---|---|
| 111565550 | apolipoprotein Da, duplicate 1 |
| 111563999 | four and a half LIM domains protein 2-like |
| 111579034 | glycoprotein (transmembrane) nmb |
| 111582421 | purine nucleoside phosphorylase 4a |
| 111579411 | uncharacterized si:ch211-256m1.8 |
| 111572570 | solute carrier family 2 member 15a |
| 111577709 | dual oxidase 2 |
| 111577711 | dual oxidase |
| 111577940 | ALK and LTK ligand 2b |
| entrez_ID | description |
|---|---|
| 111568804 | bone gamma-carboxyglutamate (gla) protein |
| 111586092 | calumenin a |
| 111588590 | collagen, type I, alpha 1a |
| 111579186 | collagen, type I, alpha 1b |
| 111573347 | collagen, type I, alpha 2 |
| 111566038 | periostin |
| 111563675 | periostin, osteoblast specific factor b |
| 111583782 | Sp7 transcription factor |
| 111573268 | collagen, type X, alpha 1a |
| 111580793 | secreted phosphoprotein 2 |
| 111564978 | upper zone of growth plate and cartilage matrix associated a |
| entrez_ID | description |
|---|---|
| 111579646 | arrestin 3b, retinal (X-arrestin) |
| 111581093 | cyclic nucleotide gated channel subunit alpha 3a |
| 111584765 | guanine nucleotide binding protein (G protein), alpha transducing activity polypeptide 1 |
| 111584041 | guanylate cyclase activator 1A |
| 111580086 | phosphodiesterase 6A, cGMP-specific, rod, alpha |
| 111581810 | retinal cone rhodopsin-sensitive cGMP 3’,5’-cyclic phosphodiesterase subunit gamma-like.4 |
| 111575698 | sodium/potassium/calcium exchanger 2-like.1 |
| entrez_ID | description |
|---|---|
| 111566251 | high affinity choline transporter 1-like |
| 111566253 | high-affinity choline transporter 1-like.1 |
| 111577330 | high-affinity choline transporter 1-like.3 |
| 111583962 | high-affinity choline transporter 1-like.5 |
| 111581877 | cholinergic receptor, nicotinic, alpha 1 (muscle) |
| 111567659 | cholinergic receptor, nicotinic, gamma |
| 111588831 | collagen-like tail subunit (single strand of homotrimer) of asymmetric acetylcholinesterase |
| entrez_ID | description |
|---|---|
| 111564800 | acetoacetyl-CoA synthetase |
| 111570356 | 3-hydroxy-3-methylglutaryl-CoA synthase 1 (soluble) |
| 111579328 | 3-hydroxy-3-methylglutaryl-coenzyme A reductase-like.1 |
| 111568310 | mevalonate kinase |
| 111577166 | mevalonate (diphospho) decarboxylase a |
| 111565278 | isopentenyl-diphosphate delta isomerase 1 |
| 111571978 | farnesyl diphosphate synthase (farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase) |
| 111569937 | farnesyl-diphosphate farnesyltransferase 1 |
| 111562938 | squalene epoxidase a |
| 111582860 | lanosterol synthase (2,3-oxidosqualene-lanosterol cyclase) |
| 111581125 | 24-dehydrocholesterol reductase |
| 111565075 | lanosterol 14-alpha demethylase |
| 111574709 | methylsterol monooxygenase 1 |
| 111565582 | NAD(P) dependent steroid dehydrogenase-like |
| 111574572 | ergosterol biosynthesis 28 homolog |
| 111580686 | EBP cholestenol delta-isomerase |
| 111584459 | EBP like |
| 111573906 | stearoyl-CoA desaturase b |
| 111583785 | sterol O-acyltransferase 2 |
| 111568530 | cholesterol 25-hydroxylase |
| 111563276 | vitamin D 25-hydroxylase |
| 111587639 | 25-hydroxyvitamin D-1 alpha hydroxylase, mitochondrial |
| 111579624 | 1,25-dihydroxyvitamin D(3) 24-hydroxylase, mitochondrial |
| 111565886 | vitamin D3 receptor B |
| entrez_ID | description |
|---|---|
| 111570570 | hydroxy-delta-5-steroid dehydrogenase, 3 beta- and steroid delta-isomerase 1 |
| 111575402 | progesterone receptor |
| 111567954 | hydroxysteroid (11-beta) dehydrogenase 2 |
| 111565142 | nuclear receptor subfamily 3, group C, member 1 (glucocorticoid receptor) |
| 111574492 | glucocorticoid receptor |
| 111576668 | hydroxysteroid (17-beta) dehydrogenase 3 |
| 111572734 | hydroxysteroid (17-beta) dehydrogenase 14 |
| 111569843 | steroid-5-alpha-reductase, alpha polypeptide 1 (3-oxo-5 alpha-steroid delta 4-dehydrogenase alpha 1) |
| 111587360 | androgen receptor |
| 111565746 | aromatase |
| 111588998 | estrogen receptor 2a |
| entrez_ID | description |
|---|---|
| 111576985 | cytochrome P450 7A1 |
| 111568649 | 5-beta-cholestane-3-alpha,7-alpha-diol 12-alpha-hydroxylase-like |
| 111568654 | 5-beta-cholestane-3-alpha,7-alpha-diol 12-alpha-hydroxylase-like.1 |
| 111573167 | aldo-keto reductase family 1 member D1-like |
| 111568532 | sterol 26-hydroxylase, mitochondrial.1 |
| 111563882 | uncharacterized LOC111563882 |
| 111577715 | hsFATP2a_ACSVL_like domain-containing protein |
| 111564846 | alpha-methylacyl-CoA racemase |
| 111564685 | hydroxysteroid (17-beta) dehydrogenase 4 |
| 111587618 | sterol carrier protein 2a |
| 111576150 | sterol carrier protein 2b |
| 111569566 | acyl-CoA thioesterase 20 |
| 111572824 | ATP-binding cassette, sub-family B (MDR/TAP), member 11a |
| entrez_ID | description |
|---|---|
| 111580133 | uncharacterized protein C7orf50 homolog |
| 111567927 | G protein-coupled receptor 146 |
| 111578189 | sterol regulatory element binding transcription factor 1 |
| 111583833 | sterol regulatory element binding transcription factor 2 |
| 111581423 | ER lipid raft associated 1 |
| 111588229 | ER lipid raft associated 2 |
| 111571031 | nuclear receptor subfamily 1, group H, member 3 |
| 111579104 | antifreeze protein type IV |
| 111574547 | apolipoprotein A-Ib |
| 118469590 | apolipoprotein A-II |
| 111562603 | apolipoprotein A-IV a |
| 111562606 | apolipoprotein A-IV-like |
| 111588528 | apolipoprotein A-IV-like.1 |
| 111575002 | phospholipid-transporting ATPase ABCA1-like.1 |
| 111570931 | ATP-binding cassette, sub-family A (ABC1), member 1B |
| 111565691 | phospholipid-transporting ATPase ABCA1-like |
| 111580395 | scavenger receptor class B, member 2a |
| 111583031 | scavenger receptor class B, member 2c |
| 111572688 | NPC intracellular cholesterol transporter 2 |
| 111588691 | ATP-binding cassette, sub-family G (WHITE), member 1 |
| 111580988 | lecithin-cholesterol acyltransferase |
| 111578413 | lipase, hepatic a |
| 111568009 | low density lipoprotein receptor-related protein 1Ab |
| 111575117 | low density lipoprotein receptor-related protein 1Bb |
| 111587369 | low-density lipoprotein receptor-related protein 1-like |
| 111564477 | syndecan 4 |
| 111586529 | syndecan-4-like |
| 111569004 | cholesteryl ester transfer protein, plasma |
| 111574222 | acetyl-CoA acetyltransferase 2 |
| 111563899 | sterol O-acyltransferase 1 |
| 111583785 | sterol O-acyltransferase 2 |
| 111575319 | microsomal triglyceride transfer protein |
| 111586299 | apolipoprotein Ba |
| 111566432 | apolipoprotein Bb, tandem duplicate 1 |
| 111588529 | apolipoprotein C-II |
| 111562605 | apolipoprotein Ea |
| 111588526 | apolipoprotein Eb |
| 111566387 | low density lipoprotein receptor a |
| 111567577 | myosin regulatory light chain interacting protein a |
| 111581127 | proprotein convertase subtilisin/kexin type 9 |
| 111573603 | Niemann-Pick disease, type C1 |
| 111572824 | ATP-binding cassette, sub-family B (MDR/TAP), member 11a |
| 111585084 | lipoprotein lipase a |
| 111586568 | lipoprotein lipase |
| 111567821 | lipase, endothelial |
| 111571946 | lipase maturation factor 2a |
| entrez_ID | description |
|---|---|
| 111580890 | alpha-2-macroglobulin-like |
| 111580892 | alpha-2-macroglobulin-like.1 |
| 111580894 | alpha-2-macroglobulin-like.2 |
| 111580895 | alpha-2-macroglobulin-like.3 |
| 111578413 | lipase, hepatic a |
| 111578802 | transferrin-a |
| 111565453 | plasminogen |
| 111582600 | ceruloplasmin |
| 111584065 | complement C3 |
| 111583320 | coagulation factor IX |
| 111570235 | selenoprotein P2 |
| 111568029 | serpin peptidase inhibitor, clade F (alpha-2 antiplasmin, pigment epithelium derived factor), member 2a |
| entrez_ID | description |
|---|---|
| 111578837 | catalase |
| 111575864 | superoxide dismutase 1, soluble |
| 111574223 | superoxide dismutase 2, mitochondrial |
| 111575331 | extracellular superoxide dismutase [Cu-Zn] |
| 111575353 | copper chaperone for superoxide dismutase |
| 111577687 | glutathione peroxidase 3 |
| 111563473 | glutathione peroxidase 4a |
| 111571007 | phospholipid hydroperoxide glutathione peroxidase-like |
| 111582504 | glutathione peroxidase 7 |
| 111580757 | glutathione peroxidase 8 (putative) |
| 111567860 | glutathione peroxidase 9 |
| 111569366 | NAD(P)H dehydrogenase, quinone 1 |
| 111575507 | heme oxygenase 1a |
| 111584778 | heme oxygenase-like |
| 111569915 | heme oxygenase 2a |
| 111567707 | heme oxygenase 2b |
| 111565959 | UDP-glucuronosyltransferase 1-2-like |
| 111568569 | UDP glycosyltransferase 8 |
| 111571828 | UDP-glucuronosyltransferase-like |
| 111580426 | UDP glucuronosyltransferase 2 family, polypeptide B3 |
| 111566481 | glutamate-cysteine ligase, catalytic subunit |
| 111586211 | biliverdin reductase B |
| 111570618 | glutamate-cysteine ligase, modifier subunit |
| 111573235 | epoxide hydrolase 2, cytoplasmic |
| 111572235 | epoxide hydrolase 4 |
| 111585235 | epoxide hydrolase 5 |
| 111572118 | sulfiredoxin 1 homolog (S. cerevisiae) |
| 111572824 | ATP-binding cassette, sub-family B (MDR/TAP), member 11a |
| 111562997 | liver carboxylesterase 1-like |
| 111569059 | carboxylesterase 3 |
| 111577847 | nfe2 like bZIP transcription factor 2a |
| 111570165 | kelch-like ECH-associated protein 1b |
| entrez_ID | description |
|---|---|
| 111563068 | C-X-C motif chemokine 13-like |
| 111569545 | C-X-C motif chemokine 3-like |
| 111562955 | chemokine (C-X-C motif) receptor 3, tandem duplicate 1 |
| 111577429 | C-X-C motif chemokine 5-like |
| 111586938 | cyclic GMP-AMP synthase a |
| 111563935 | cyclic GMP-AMP synthase |
| 111584798 | DEXH (Asp-Glu-X-His) box polypeptide 58 |
| 111567610 | stimulator of interferon response cGAMP interactor 1 |
| 111576250 | zinc finger, NFX1-type containing 1 |
| 111573712 | eukaryotic translation initiation factor 2-alpha kinase 2 |
| 111573734 | interferon-induced, double-stranded RNA-activated protein kinase-like.1 |
| 111588694 | cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial |
| 111588695 | radical S-adenosyl methionine domain containing 2 |
| 111562645 | cytosolic 5’-nucleotidase 1A-like |
| 111584600 | interferon regulatory factor 3 |
| 111574762 | interferon-induced GTP-binding protein Mx |
| 111574765 | interferon-induced GTP-binding protein Mx-like |
| 111585454 | interferon-induced protein with tetratricopeptide repeats 5-like |
| 129347476 | interferon-induced protein with tetratricopeptide repeats 5-like.1 |
| 111562649 | interferon alpha-inducible protein 27-like protein 2A |
| 111577915 | interferon alpha-inducible protein 27-like protein 2A.2 |
| 111588558 | ISG15 ubiquitin like modifier |
| 111584047 | ubiquitin specific peptidase 18 |
| 111582159 | E3 ubiquitin-protein ligase NEURL3 |
| 118471831 | interferon gamma 1 |
| 111572427 | signal transducer and activator of transcription 1a |
| 111566617 | signal transducer and activator of transcription 2 |
| entrez_ID | description |
|---|---|
| 111571778 | E2F transcription factor 1 |
| 111563434 | ATR serine/threonine kinase |
| 111580652 | checkpoint kinase 1 |
| 111564411 | cyclin B2 |
| 111576335 | WEE1 G2 checkpoint kinase |
| 111579731 | cyclin-dependent kinase 2 |
| 111578176 | cyclin A2 |
| 111574031 | cyclin E1 |
| 111582432 | cyclin E2 |
| 111569251 | G1/S-specific cyclin-E2-like |
| 111576022 | DNA repair protein XRCC4-like |
| 111568731 | FA complementation group A |
| 111585542 | FA complementation group B |
| 111576667 | FA complementation group C |
| 111566993 | FA complementation group E |
| 111584863 | FA complementation group G |
| 111563082 | FA complementation group I |
| 111567306 | BRCA1 DNA repair associated |
| 111587086 | retinoblastoma binding protein 8 |
| 111572887 | BRCA1 associated RING domain 1 |
| 111566265 | partner and localizer of BRCA2 |
| 111581756 | RAD52 motif containing 1 |
| 111588143 | RAD52 homolog, DNA repair protein |
| 111579911 | centromere protein S |
| 111577714 | FANCD2 and FANCI associated nuclease 1 |
| 111581512 | nei-like DNA glycosylase 3 |
| 111588554 | uracil DNA glycosylase a |
| 111588339 | APEX nuclease (apurinic/apyrimidinic endonuclease) 2 |
| 111574625 | ligase I, DNA, ATP-dependent |
| 111571989 | flap structure-specific endonuclease 1 |
| 111587039 | ETAA1 activator of ATR kinase a |
| 111569726 | replication protein A1 |
| 111563381 | replication protein A2 |
| 111577896 | mutS homolog 2 (E. coli) |
| 111586691 | exonuclease 1 |
| entrez_ID | description |
|---|---|
| 111565606 | C-C motif chemokine 21-like |
| 111565785 | interferon-induced protein 44-like |
| 111569545 | C-X-C motif chemokine 3-like |
| 111565603 | C-C motif chemokine 19-like |
| 129350609 | receptor-transporting protein 3-like.1 |
| 111566617 | signal transducer and activator of transcription 2 |
| 111584583 | transporter associated with antigen processing, subunit type a |
| 111562713 | XIAP associated factor 1 |
| 111571519 | protein mono-ADP-ribosyltransferase PARP11.1 |
| 111584589 | H-2 class I histocompatibility antigen, Q9 alpha chain |
| 111569157 | suppressor of cytokine signaling 1-like |
| 111586660 | sorting nexin 20 |
| 111574043 | interferon-induced protein 44-like.2 |
| 111588744 | interferon regulatory factor 10 |
| entrez_ID | description |
|---|---|
| 111574818 | hemoglobin embryonic subunit alpha-like.1 |
| 111582400 | hemoglobin beta embryonic-2 |
| 111570155 | myoglobin |
| 111585684 | anterior gradient 2 |
| 111581053 | proproteinase E-like |
| 111582409 | aquaporin 8a, tandem duplicate 2 |
| 111579739 | acidic mammalian chitinase-like.4 |
| entrez_ID | description |
|---|---|
| 111574812 | hemoglobin embryonic subunit alpha-like |
| 111574813 | hemoglobin embryonic subunit alpha.1 |
| 111574814 | hemoglobin subunit beta-like.2 |
| 111574811 | hemoglobin embryonic subunit alpha |
| 111566442 | apolipoprotein B-100-like.1 |
| 111566432 | apolipoprotein Bb, tandem duplicate 1 |
| 111564925 | fatty acid synthase |
| 111570821 | acyl-CoA synthetase short chain family member 2 like |
| 111566479 | ELOVL fatty acid elongase 5 |
| 111588379 | ELOVL fatty acid elongase 6 |
| 111571760 | acetyl-CoA carboxylase alpha |
| 111564800 | acetoacetyl-CoA synthetase |
🔎 For differential expression , gene expression is rarely considered at the level of raw counts since libraries sequenced at a greater depth will result in higher counts. Rather, it is common practice to transform raw counts onto a scale that accounts for such library size differences. Popular transformations include counts per million (CPM), log2-counts per million (log-CPM), reads per kilobase of transcript per million (RPKM), and fragments per kilobase of transcript per million (FPKM). Here raw counts are converted log-CPM values using the voom function in limma package.
What is voom doing? Counts are transformed to log2 counts per million reads (CPM), where “per million reads” is defined based on the normalization factors we calculated earlier A linear model is fitted to the log2 CPM for each gene, and the residuals are calculated A smoothed curve is fitted to the sqrt(residual standard deviation) by average expression (see red line in plot above) The smoothed curve is used to obtain weights for each gene and sample that are passed into limma along with the log2 CPMs.
* Step 2: We can now process our original
(filtered, TMM-normalised) object through the voom-limma pipeline, which
will normalised it by library size by calculating logCPM and using the
normalisation factors provided, and then fit a linear model through
it:
Notice how I could not quite reproduce the limma-lmFit calculated sigma values. (compare with manually generated ones in plot just next to it). Will need to figure out the details of the limma sigma calculation.
treatmentCPF treatmentCPF.T3IOP treatmentDMSO treatmentMPI treatmentT3IOP
111562382 4.597323 4.588862 4.293602 4.433082 4.687885
111562384 3.716782 3.602682 3.123277 3.430930 3.273383
111562387 5.126211 5.252706 5.210131 5.123160 5.278484
111562388 4.024122 3.740996 3.638425 3.674899 3.499010
111562389 3.383426 3.445715 3.510595 3.557256 3.479879
111562390 5.587841 5.711669 5.863940 5.750005 5.616157
Contrasts
Levels treatmentCPF - treatmentDMSO
treatmentCPF 1
treatmentCPF.T3IOP 0
treatmentDMSO -1
treatmentMPI 0
treatmentT3IOP 0
Below, a list of all the genes that appear significantly
differently expressed between treatment and control (in either
direction; Table 1). In Table 2, the
subest of significantly changing genes whose fold-change is bigger than
2folds (in either direction). These genes are ranked in order of
decreasing fold change.
[1] "1477 differentially expressed genes (P <0.05, FC<1/2 OR FC>2):"
[1] "715 genes upregulated by CPF"
[1] "762 genes downregulated by CPF"
🔎 Can we get some broad ideas of the families of genes represented by the genes we have found to be differentially expressed? In our ranked list of Differentially Expressed genes, are some pathways/biological processes over-represented? We will use the clusterProfileR/enricheR packages for a first analysis.
* Top over-represented Gene Ontology gene sets (ordered by
adjusted p.value, descending):
Scale for fill is already present.
Adding another scale for fill, which will replace the existing scale.
* … and genes associated with it (notice the overlaps of genes
belonging to multiple sets):
* Relationship between the Gene sets identified:
Warning: Use 'cex.params = list(category_node = your_value)' instead of 'cex_category'.
The cex_category parameter will be removed in the next version.Warning: Use 'cex.params = list(category_label = your_value)' instead of 'cex_label_category'.
The cex_label_category parameter will be removed in the next version.Warning: Use 'cex.params = list(line = your_value)' instead of 'cex_line'.
The cex_line parameter will be removed in the next version.
* Quantification of the overlap between genes in each set:
Warning: `aes_()` was deprecated in ggplot2 3.0.0.
Please use tidy evaluation idioms with `aes()`
Below, a list of the pathway identified by Gene Enrichment
Analysis, and the genes in our differential-expression list that belong
to each:
🔎 Complementarily, we can perform Gene Set Enrichment Analysis (GSE), not on just the genes we have found to be truly Differentially Expressed (i.e. significant, fold change above a given threshold), but on all genes found to differ between the two timepoints. GSE will look for genes showing significantly co-ordinated shifts in expression across the timepoints, regardless of their magnitude, and indicate the Gene Ontology family to which they most belong.
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 85 | 7.078257 | 0.0000000 | ENSAOCG00000011966 | interferon regulatory factor 7 | 4.1135866 | 2.0489941 | 3.5977941 |
| 120 | 5.754260 | 0.0000000 | ENSAOCG00000006804 | interferon regulatory factor 10 | 2.0014121 | 1.3915907 | 3.6576699 |
| 262 | 3.854722 | 0.0000000 | ENSAOCG00000009800 | c-Myc-binding protein-like | 0.8264786 | 1.0624104 | 2.8308431 |
| 307 | 3.541154 | 0.0000006 | ENSAOCG00000001429 | HMG box-containing protein 1-like | 3.0884039 | 0.8723342 | 2.7761048 |
| 315 | 3.492513 | 0.0000862 | ENSAOCG00000016636 | cAMP-responsive element modulator-like | -0.4351943 | 0.5776825 | 3.0308485 |
| 418 | -3.117339 | 0.0000000 | ENSAOCG00000016021 | E2F transcription factor 8 | 3.9912401 | -2.0957846 | -1.1848456 |
| 440 | -3.060661 | 0.0000000 | ENSAOCG00000015259 | E2F transcription factor 7 | 2.9108956 | -2.0877202 | -1.1399665 |
| 568 | 2.790445 | 0.0000000 | ENSAOCG00000004648 | interferon regulatory factor 8 | 2.8819942 | 0.8378111 | 2.1231795 |
| 746 | 2.536091 | 0.0000000 | ENSAOCG00000006661 | forkhead box D3 | 2.8712268 | 0.8501477 | 1.8350648 |
| 884 | 2.388997 | 0.0000015 | ENSAOCG00000010889 | HMG-box transcription factor 1 | 5.1284569 | 0.5707727 | 1.9420380 |
| 1008 | 2.294870 | 0.0016737 | ENSAOCG00000011299 | vitamin D3 receptor B | 2.7471716 | 0.1727746 | 2.2240507 |
| 1043 | 2.271704 | 0.0000000 | ENSAOCG00000013898 | transcription factor EB | 4.5670032 | 0.7845373 | 1.5830122 |
| 1109 | -2.231082 | 0.0000000 | ENSAOCG00000012367 | forkhead box M1 | 2.6648268 | -1.5758511 | -0.7396363 |
| 1129 | -2.220877 | 0.0000000 | ENSAOCG00000016070 | E2F transcription factor 2 | 2.7464877 | -1.5784350 | -0.7238244 |
| 1146 | 2.206853 | 0.0000000 | ENSAOCG00000014976 | activating transcription factor 3 | 4.7983858 | 0.6616465 | 1.6223343 |
| 1151 | -2.203311 | 0.0000000 | ENSAOCG00000000956 | E2F transcription factor 1 | 3.3531519 | -1.6511179 | -0.6282281 |
| 1445 | 2.049281 | 0.0000000 | ENSAOCG00000009059 | cAMP-responsive element modulator-like.1 | 4.9011754 | 0.6498377 | 1.4203973 |
| 1486 | 2.029369 | 0.0001288 | ENSAOCG00000002749 | transcription factor HES-1-like | 0.7599566 | 0.3082510 | 1.7338117 |
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 15 | 31.193419 | 0.0000000 | ENSAOCG00000021849 | C-C motif chemokine 21-like | 3.9229597 | 3.1647198 | 6.7616198 |
| 43 | 10.857986 | 0.0000000 | ENSAOCG00000021807 | C-C motif chemokine 19-like | 2.6373316 | 1.8801146 | 5.0012546 |
| 140 | 5.237432 | 0.0000006 | ENSAOCG00000021393 | fibroblast growth factor 19 | 0.5031300 | 1.1402542 | 3.6374652 |
| 161 | 4.834595 | 0.0000000 | ENSAOCG00000000350 | C-X-C motif chemokine 3-like | 0.1732039 | 1.2774156 | 3.2693747 |
| 328 | 3.420514 | 0.0000000 | ENSAOCG00000002726 | insulin receptor substrate 2-like | 6.1365065 | 1.1646180 | 2.3838084 |
| 365 | 3.284270 | 0.0000306 | ENSAOCG00000017689 | interleukin-1 beta-like | 2.6769081 | 0.6215557 | 2.8095896 |
| 527 | -2.877372 | 0.0000000 | ENSAOCG00000001825 | urotensin-2-like | 1.7290122 | -2.1252227 | -0.9242804 |
| 616 | 2.722411 | 0.0000000 | ENSAOCG00000016852 | fibroblast growth factor 7 | 1.9933149 | 0.9771695 | 1.9126004 |
| 624 | 2.713739 | 0.0007007 | ENSAOCG00000006664 | C-X-C motif chemokine 13-like | -1.4880440 | 0.2988652 | 2.5816988 |
| 698 | 2.588272 | 0.0000002 | ENSAOCG00000005792 | chemerin-like receptor 1 | 0.7048903 | 0.6874396 | 2.0565394 |
| 944 | -2.349010 | 0.0000090 | ENSAOCG00000001578 | parathyroid hormone-related protein-like | -0.2685769 | -1.9660141 | -0.4980916 |
| 952 | 2.340531 | 0.0000000 | ENSAOCG00000017457 | neurotensin | 1.1032705 | 0.6574539 | 1.7962181 |
| 1147 | -2.206435 | 0.0000000 | ENSAOCG00000021414 | fibroblast growth factor 4 | 1.1640865 | -1.5851199 | -0.6983148 |
| 1205 | 2.172111 | 0.0000000 | ENSAOCG00000013198 | cellular communication network factor 5 | 2.8327025 | 0.6817869 | 1.5564084 |
| 1277 | 2.127529 | 0.0010447 | ENSAOCG00000005622 | interleukin-8-like | 2.7417705 | 0.1960192 | 1.9823386 |
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 15 | 31.193419 | 0.0000000 | ENSAOCG00000021849 | C-C motif chemokine 21-like | 3.9229597 | 3.1647198 | 6.761620 |
| 43 | 10.857986 | 0.0000000 | ENSAOCG00000021807 | C-C motif chemokine 19-like | 2.6373316 | 1.8801146 | 5.001255 |
| 161 | 4.834595 | 0.0000000 | ENSAOCG00000000350 | C-X-C motif chemokine 3-like | 0.1732039 | 1.2774156 | 3.269375 |
| 624 | 2.713739 | 0.0007007 | ENSAOCG00000006664 | C-X-C motif chemokine 13-like | -1.4880440 | 0.2988652 | 2.581699 |
| 1277 | 2.127529 | 0.0010447 | ENSAOCG00000005622 | interleukin-8-like | 2.7417705 | 0.1960192 | 1.982339 |
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 15 | 31.193419 | 0.0000000 | ENSAOCG00000021849 | C-C motif chemokine 21-like | 3.9229597 | 3.1647198 | 6.761620 |
| 43 | 10.857986 | 0.0000000 | ENSAOCG00000021807 | C-C motif chemokine 19-like | 2.6373316 | 1.8801146 | 5.001255 |
| 161 | 4.834595 | 0.0000000 | ENSAOCG00000000350 | C-X-C motif chemokine 3-like | 0.1732039 | 1.2774156 | 3.269375 |
| 365 | 3.284270 | 0.0000306 | ENSAOCG00000017689 | interleukin-1 beta-like | 2.6769081 | 0.6215557 | 2.809590 |
| 624 | 2.713739 | 0.0007007 | ENSAOCG00000006664 | C-X-C motif chemokine 13-like | -1.4880440 | 0.2988652 | 2.581699 |
| 1277 | 2.127529 | 0.0010447 | ENSAOCG00000005622 | interleukin-8-like | 2.7417705 | 0.1960192 | 1.982339 |
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 2 | 106.108271 | 0.0001077 | ENSAOCG00000009483 | radical S-adenosyl methionine domain containing 2 | 0.7886398 | 2.0874194 | 11.371367 |
| 198 | 4.398012 | 0.0000000 | ENSAOCG00000014773 | interferon induced with helicase C domain 1 | 4.5326141 | 1.3361004 | 2.937603 |
| 490 | 2.954210 | 0.0000000 | ENSAOCG00000014324 | stimulator of interferon response cGAMP interactor 1 | 4.7936445 | 1.1099843 | 2.015561 |
| 749 | 2.533225 | 0.0000000 | ENSAOCG00000003018 | BPI fold containing family C, like | 3.4556548 | 0.8807504 | 1.801201 |
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 42 | 11.208823 | 0.0000141 | ENSAOCG00000001507 | F-box protein 32 | 3.685539 | 1.3591410 | 5.6139848 |
| 290 | 3.623111 | 0.0000000 | ENSAOCG00000021490 | probable E3 ubiquitin-protein ligase RNF144A-A | 2.561224 | 1.1396744 | 2.5747837 |
| 364 | 3.288402 | 0.0000000 | ENSAOCG00000003430 | ankyrin repeat and SOCS box protein 5-like | 3.874505 | 1.1363472 | 2.2984258 |
| 421 | 3.110220 | 0.0009412 | ENSAOCG00000021104 | ankyrin repeat and SOCS box containing 10 | 1.666977 | 0.3069065 | 2.9671270 |
| 443 | 3.056145 | 0.0000002 | ENSAOCG00000009597 | uncharacterized LOC111578154 | 1.780247 | 0.8114182 | 2.4120082 |
| 889 | 2.386079 | 0.0000000 | ENSAOCG00000009911 | F-box protein 25 | 1.852955 | 0.6994113 | 1.8098728 |
| 1222 | 2.165001 | 0.0000000 | ENSAOCG00000014883 | suppressor of cytokine signaling 3-like | 5.249281 | 0.7054199 | 1.5233148 |
| 1239 | -2.153274 | 0.0000000 | ENSAOCG00000020444 | pre-mRNA processing factor 19 | 5.726295 | -1.4976596 | -0.7154035 |
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 2 | 106.108271 | 0.0001077 | ENSAOCG00000009483 | radical S-adenosyl methionine domain containing 2 | 0.7886398 | 2.0874194 | 11.371367 |
| 198 | 4.398012 | 0.0000000 | ENSAOCG00000014773 | interferon induced with helicase C domain 1 | 4.5326141 | 1.3361004 | 2.937603 |
| 749 | 2.533225 | 0.0000000 | ENSAOCG00000003018 | BPI fold containing family C, like | 3.4556548 | 0.8807504 | 1.801201 |
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 364 | 3.288402 | 0.0000000 | ENSAOCG00000003430 | ankyrin repeat and SOCS box protein 5-like | 3.874505 | 1.1363472 | 2.298426 |
| 421 | 3.110220 | 0.0009412 | ENSAOCG00000021104 | ankyrin repeat and SOCS box containing 10 | 1.666977 | 0.3069065 | 2.967127 |
| 1222 | 2.165001 | 0.0000000 | ENSAOCG00000014883 | suppressor of cytokine signaling 3-like | 5.249281 | 0.7054199 | 1.523315 |
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 85 | 7.078257 | 0 | ENSAOCG00000011966 | interferon regulatory factor 7 | 4.1135866 | 2.0489941 | 3.597794 |
| 120 | 5.754260 | 0 | ENSAOCG00000006804 | interferon regulatory factor 10 | 2.0014121 | 1.3915907 | 3.657670 |
| 262 | 3.854722 | 0 | ENSAOCG00000009800 | c-Myc-binding protein-like | 0.8264786 | 1.0624104 | 2.830843 |
| 568 | 2.790445 | 0 | ENSAOCG00000004648 | interferon regulatory factor 8 | 2.8819942 | 0.8378111 | 2.123179 |
| FC | adj.P.Val | ensembl_ID | merged_description | AveExpr | CI.L | CI.R | |
|---|---|---|---|---|---|---|---|
| 365 | 3.28427 | 3.06e-05 | ENSAOCG00000017689 | interleukin-1 beta-like | 2.676908 | 0.6215557 | 2.80959 |
An alternative analysis of gene-set enrichment is Model-based Gene Set Analysis, which tries to find the most conservative set of Gene Ontology gene sets that covers the genes submitted for analysis (in this case, the differentially expressed genes). In theory, the resulting Gene Sets will be less redundant than previous approaches.
The Gene sets with highest probability of activation are:
Below, for reference, the scoring of all Gene Ontology gene
sets considered, and the hyperparameters of the model ( alpha ,
beta, and indirectly p ):
For the top scoring pathways, below the list of the actual
genes belonging to that pathway that were found in our list of
differentially-expressed genes:
| p.value | id | database | description | adjusted_pvalue | |
|---|---|---|---|---|---|
| 662 | 0.0000190 | GO:0006270 | GO | DNA replication initiation | 0.0000153 |
| 153 | 0.0002441 | GO:0051603 | GO | proteolysis involved in protein catabolic process | 0.0000305 |
| 451 | 0.0004972 | GO:0051225 | GO | spindle assembly | 0.0000458 |
| 127 | 0.0006862 | GO:0006261 | GO | DNA-templated DNA replication | 0.0000610 |
| 1420 | 0.0016776 | GO:0036297 | GO | interstrand cross-link repair | 0.0000763 |
| 1565 | 0.0031825 | GO:0030261 | GO | chromosome condensation | 0.0000915 |
| 1776 | 0.0058595 | GO:0051382 | GO | kinetochore assembly | 0.0001068 |
| 855 | 0.0060320 | GO:0051321 | GO | meiotic cell cycle | 0.0001221 |
| 2034 | 0.0061692 | GO:0009157 | GO | deoxyribonucleoside monophosphate biosynthetic process | 0.0001373 |
| 102 | 0.0068306 | GO:0010906 | GO | regulation of glucose metabolic process | 0.0001526 |
| 658 | 0.0072105 | GO:0009615 | GO | response to virus | 0.0001678 |
| 480 | 0.0087610 | GO:0015671 | GO | oxygen transport | 0.0001831 |
| 2445 | 0.0090578 | GO:0031297 | GO | replication fork processing | 0.0001984 |
| 1067 | 0.0096332 | GO:0032446 | GO | protein modification by small protein conjugation | 0.0002136 |
| 126 | 0.0121840 | GO:0006269 | GO | DNA replication, synthesis of RNA primer | 0.0002289 |
| 1485 | 0.0124179 | GO:0002573 | GO | myeloid leukocyte differentiation | 0.0002441 |
| 1090 | 0.0138946 | GO:0000070 | GO | mitotic sister chromatid segregation | 0.0002594 |
| 730 | 0.0145327 | GO:0006569 | GO | tryptophan catabolic process | 0.0002746 |
| 837 | 0.0147286 | GO:0051276 | GO | chromosome organization | 0.0002899 |
| 1342 | 0.0149019 | GO:0006207 | GO | ‘de novo’ pyrimidine nucleobase biosynthetic process | 0.0003052 |
| 1178 | 0.0151171 | GO:0006621 | GO | protein retention in ER lumen | 0.0003204 |
| 2656 | 0.0161531 | GO:0001837 | GO | epithelial to mesenchymal transition | 0.0003357 |
| 1450 | 0.0165842 | GO:0019287 | GO | isopentenyl diphosphate biosynthetic process, mevalonate pathway | 0.0003509 |
| 1767 | 0.0167932 | GO:0007076 | GO | mitotic chromosome condensation | 0.0003662 |
| 1195 | 0.0168562 | GO:0008630 | GO | intrinsic apoptotic signaling pathway in response to DNA damage | 0.0003814 |
| 2290 | 0.0174160 | GO:0006839 | GO | mitochondrial transport | 0.0003967 |
| 317 | 0.0190975 | GO:0000387 | GO | spliceosomal snRNP assembly | 0.0004120 |
| 2260 | 0.0202995 | GO:0036066 | GO | protein O-linked fucosylation | 0.0004272 |
| 2206 | 0.0208556 | GO:0098542 | GO | defense response to other organism | 0.0004425 |
| 729 | 0.0219236 | GO:0019441 | GO | tryptophan catabolic process to kynurenine | 0.0004577 |
We can do the same with KEGG pathways
| p.value | id | database | description | adjusted_pvalue | index | |
|---|---|---|---|---|---|---|
| 15 | 0.0000000 | aoce00190 | KEGG | Oxidative phosphorylation - Amphiprion ocellaris (clown anemonefish) | 0.0002890 | 1 |
| 86 | 0.0000000 | aoce01100 | KEGG | Metabolic pathways - Amphiprion ocellaris (clown anemonefish) | 0.0005780 | 2 |
| 124 | 0.0000000 | aoce04110 | KEGG | Cell cycle - Amphiprion ocellaris (clown anemonefish) | 0.0008671 | 3 |
| 102 | 0.0000000 | aoce03030 | KEGG | DNA replication - Amphiprion ocellaris (clown anemonefish) | 0.0011561 | 4 |
| 104 | 0.0000000 | aoce03050 | KEGG | Proteasome - Amphiprion ocellaris (clown anemonefish) | 0.0014451 | 5 |
| 103 | 0.0000000 | aoce03040 | KEGG | Spliceosome - Amphiprion ocellaris (clown anemonefish) | 0.0017341 | 6 |
| 113 | 0.0000000 | aoce03430 | KEGG | Mismatch repair - Amphiprion ocellaris (clown anemonefish) | 0.0020231 | 7 |
| 116 | 0.0000000 | aoce03460 | KEGG | Fanconi anemia pathway - Amphiprion ocellaris (clown anemonefish) | 0.0023121 | 8 |
| 114 | 0.0000001 | aoce03440 | KEGG | Homologous recombination - Amphiprion ocellaris (clown anemonefish) | 0.0026012 | 9 |
| 64 | 0.0000005 | aoce00630 | KEGG | Glyoxylate and dicarboxylate metabolism - Amphiprion ocellaris (clown anemonefish) | 0.0028902 | 10 |
| 11 | 0.0000005 | aoce00100 | KEGG | Steroid biosynthesis - Amphiprion ocellaris (clown anemonefish) | 0.0031792 | 11 |
| 84 | 0.0000008 | aoce00983 | KEGG | Drug metabolism - other enzymes - Amphiprion ocellaris (clown anemonefish) | 0.0034682 | 12 |
| 91 | 0.0000011 | aoce01232 | KEGG | Nucleotide metabolism - Amphiprion ocellaris (clown anemonefish) | 0.0037572 | 13 |
| 112 | 0.0000021 | aoce03420 | KEGG | Nucleotide excision repair - Amphiprion ocellaris (clown anemonefish) | 0.0040462 | 14 |
| 2 | 0.0000022 | aoce00020 | KEGG | Citrate cycle (TCA cycle) - Amphiprion ocellaris (clown anemonefish) | 0.0043353 | 15 |
| 23 | 0.0000035 | aoce00280 | KEGG | Valine, leucine and isoleucine degradation - Amphiprion ocellaris (clown anemonefish) | 0.0046243 | 16 |
| 97 | 0.0000037 | aoce03013 | KEGG | Nucleocytoplasmic transport - Amphiprion ocellaris (clown anemonefish) | 0.0049133 | 17 |
| 142 | 0.0000041 | aoce04218 | KEGG | Cellular senescence - Amphiprion ocellaris (clown anemonefish) | 0.0052023 | 18 |
| 19 | 0.0000078 | aoce00240 | KEGG | Pyrimidine metabolism - Amphiprion ocellaris (clown anemonefish) | 0.0054913 | 19 |
| 111 | 0.0000084 | aoce03410 | KEGG | Base excision repair - Amphiprion ocellaris (clown anemonefish) | 0.0057803 | 20 |
| 125 | 0.0000135 | aoce04114 | KEGG | Oocyte meiosis - Amphiprion ocellaris (clown anemonefish) | 0.0060694 | 21 |
| 87 | 0.0000226 | aoce01200 | KEGG | Carbon metabolism - Amphiprion ocellaris (clown anemonefish) | 0.0063584 | 22 |
| 131 | 0.0000311 | aoce04137 | KEGG | Mitophagy - animal - Amphiprion ocellaris (clown anemonefish) | 0.0066474 | 23 |
| 99 | 0.0000384 | aoce03018 | KEGG | RNA degradation - Amphiprion ocellaris (clown anemonefish) | 0.0069364 | 24 |
| 108 | 0.0000509 | aoce03265 | KEGG | Virion - Lyssavirus - Amphiprion ocellaris (clown anemonefish) | 0.0072254 | 25 |
| 17 | 0.0000747 | aoce00230 | KEGG | Purine metabolism - Amphiprion ocellaris (clown anemonefish) | 0.0075145 | 26 |
| 110 | 0.0001301 | aoce03320 | KEGG | PPAR signaling pathway - Amphiprion ocellaris (clown anemonefish) | 0.0078035 | 27 |
| 25 | 0.0001629 | aoce00310 | KEGG | Lysine degradation - Amphiprion ocellaris (clown anemonefish) | 0.0080925 | 28 |
| 30 | 0.0001814 | aoce00380 | KEGG | Tryptophan metabolism - Amphiprion ocellaris (clown anemonefish) | 0.0083815 | 29 |
| 143 | 0.0002102 | aoce04260 | KEGG | Cardiac muscle contraction - Amphiprion ocellaris (clown anemonefish) | 0.0086705 | 30 |
Contrasts
Levels treatmentMPI - treatmentDMSO
treatmentCPF 0
treatmentCPF.T3IOP 0
treatmentDMSO -1
treatmentMPI 1
treatmentT3IOP 0
Below, a list of all the genes that appear significantly
differently expressed between treatment and control (in either
direction; Table 1). In Table 2, the
subest of significantly changing genes whose fold-change is bigger than
2folds (in either direction). These genes are ranked in order of
decreasing fold change.
[1] "721 differentially expressed genes (P <0.05, FC<1/2 OR FC>2):"
[1] "296 genes upregulated by MPI"
[1] "425 genes downregulated by MPI"
Contrasts
Levels treatmentT3IOP - treatmentDMSO
treatmentCPF 0
treatmentCPF.T3IOP 0
treatmentDMSO -1
treatmentMPI 0
treatmentT3IOP 1
Below, a list of all the genes that appear significantly
differently expressed between treatment and control (in either
direction; Table 1). In Table 2, the
subest of significantly changing genes whose fold-change is bigger than
2folds (in either direction). These genes are ranked in order of
decreasing fold change.
[1] "803 differentially expressed genes (P <0.05, FC<1/2 OR FC>2):"
[1] "558 genes upregulated by T3_IOP"
[1] "245 genes downregulated by T3_IOP"
Contrasts
Levels treatmentCPF.T3IOP - treatmentDMSO
treatmentCPF 0
treatmentCPF.T3IOP 1
treatmentDMSO -1
treatmentMPI 0
treatmentT3IOP 0
Below, a list of all the genes that appear significantly
differently expressed between treatment and control (in either
direction; Table 1). In Table 2, the
subest of significantly changing genes whose fold-change is bigger than
2folds (in either direction). These genes are ranked in order of
decreasing fold change.
[1] "1507 differentially expressed genes (P <0.05, FC<1/2 OR FC>2):"
[1] "1075 genes upregulated by CPF+T3"
[1] "432 genes downregulated by CPF+T3"
Venn intersection between CPF, T3, and MPI
Venn intersection between CPF, T3, and CPFT3IOP
Find genes in every intersection (CPF, T3IOP, MPI)
Find genes in every intersection (CPF, T3IOP, CPFT3IOP)
| entrez_ID | NCBI_symbol | NCBI_description | ensembl_ID | ensembl_symbol | ensembl_description | merged_symbol | original_merged_description | merged_description | logFC | CI.L | CI.R | AveExpr | t | P.Value | adj.P.Val | B | FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 129348303 | 129348303 | LOC129348303 | uncharacterized LOC129348303 | NA | NA | NA | LOC129348303 | uncharacterized LOC129348303 | uncharacterized LOC129348303 | -10.068848 | -13.977676 | -6.160020 | 3.1991964 | -5.111081 | 0.0000016 | 7.20e-06 | 4.9057973 | -1074.05197 |
| 118470957 | 118470957 | LOC118470957 | uncharacterized LOC118470957 | NA | NA | NA | LOC118470957 | uncharacterized LOC118470957 | uncharacterized LOC118470957 | -9.506054 | -14.438282 | -4.573826 | 1.5594816 | -3.824165 | 0.0002294 | 6.81e-04 | 0.4087158 | -727.12211 |
| 111588695 | 111588695 | rsad2 | radical S-adenosyl methionine domain containing 2 | ENSAOCG00000009483 | rsad2 | radical S-adenosyl methionine domain containing 2 | rsad2 | radical S-adenosyl methionine domain containing 2 | radical S-adenosyl methionine domain containing 2 | 8.754387 | 5.680109 | 11.828665 | 0.7886398 | 5.650177 | 0.0000002 | 9.00e-07 | 7.0320258 | 431.85001 |
| 111577915 | 111577915 | LOC111577915 | interferon alpha-inducible protein 27-like protein 2A | NA | NA | NA | LOC111577915 | interferon alpha-inducible protein 27-like protein 2A | interferon alpha-inducible protein 27-like protein 2A.2 | 8.528721 | 5.330104 | 11.727338 | 0.7634300 | 5.290554 | 0.0000007 | 3.60e-06 | 5.6193709 | 369.31839 |
| 111588653 | 111588653 | LOC111588653 | calpain-1 catalytic subunit-like | NA | NA | NA | LOC111588653 | calpain-1 catalytic subunit-like | calpain-1 catalytic subunit-like.5 | -8.430433 | -10.463852 | -6.397014 | 3.1497123 | -8.226262 | 0.0000000 | 0.00e+00 | 18.2424731 | -344.99535 |
| 111565606 | 111565606 | LOC111565606 | C-C motif chemokine 21-like | ENSAOCG00000021849 | ENSAOCG00000021849 | C-C motif chemokine 21-like | LOC111565606_ENSAOCG00000021849 | C-C motif chemokine 21-like | C-C motif chemokine 21-like | 7.655180 | 6.465892 | 8.844468 | 3.9229597 | 12.771674 | 0.0000000 | 0.00e+00 | 40.9585606 | 201.57603 |
| 111564448 | 111564448 | LOC111564448 | acidic mammalian chitinase-like | ENSAOCG00000003252 | ENSAOCG00000003252 | CHIO1, chitinase O-1, chia2/9-like | LOC111564448_ENSAOCG00000003252 | acidic mammalian chitinase-like | acidic mammalian chitinase-like.1 | -7.495890 | -8.258235 | -6.733545 | 5.1246678 | -19.509732 | 0.0000000 | 0.00e+00 | 69.4069184 | -180.50438 |
| 111568546 | 111568546 | lgals17 | galectin 17 | ENSAOCG00000023360 | ENSAOCG00000023360 | novel gene (galectin 17-like) | lgals17_ENSAOCG00000023360 | galectin 17 | galectin 17 | 7.418167 | 6.441187 | 8.395147 | 5.3118168 | 15.065744 | 0.0000000 | 0.00e+00 | 51.8013770 | 171.03729 |
| 111576250 | 111576250 | znfx1 | zinc finger, NFX1-type containing 1 | ENSAOCG00000021079 | ZNFX1 | zinc finger NFX1-type containing 1 | znfx1 | zinc finger, NFX1-type containing 1 | zinc finger, NFX1-type containing 1 | 7.309194 | 5.711657 | 8.906730 | 2.8292284 | 9.078167 | 0.0000000 | 0.00e+00 | 22.9508086 | 158.59392 |
| 111571474 | 111571474 | il4i1 | interleukin 4 induced 1 | ENSAOCG00000023672 | ENSAOCG00000023672 | L-amino-acid oxidase-like.2 | il4i1_ENSAOCG00000023672 | interleukin 4 induced 1 | interleukin 4 induced 1 | 7.246212 | 5.296486 | 9.195938 | 1.9138440 | 7.374234 | 0.0000000 | 0.00e+00 | 14.7323110 | 151.81936 |
| 111576689 | 111576689 | LOC111576689 | protein translocase subunit SecA-like | NA | NA | NA | LOC111576689 | protein translocase subunit SecA-like | protein translocase subunit SecA-like | 7.245204 | 4.470180 | 10.020229 | -1.0328861 | 5.180400 | 0.0000012 | 5.50e-06 | 5.0171681 | 151.71337 |
| 111588557 | 111588557 | LOC111588557 | polyubiquitin-like | ENSAOCG00000014693 | ENSAOCG00000014693 | polyubiquitin-like.1 | LOC111588557_ENSAOCG00000014693 | polyubiquitin-like | polyubiquitin-like | 7.185437 | 5.695307 | 8.675567 | 3.1584896 | 9.567721 | 0.0000000 | 0.00e+00 | 25.3551057 | 145.55668 |
| 118469095 | 118469095 | sb:cb1081 | sterile alpha motif domain-containing protein 9-like | NA | NA | NA | sb:cb1081 | sterile alpha motif domain-containing protein 9-like | sterile alpha motif domain-containing protein 9-like.3 | 7.184799 | 6.098363 | 8.271235 | 4.2081541 | 13.121694 | 0.0000000 | 0.00e+00 | 42.7175548 | 145.49229 |
| 111573059 | 111573059 | LOC111573059 | tyrosinase-like | NA | NA | NA | LOC111573059 | tyrosinase-like | tyrosinase-like.1 | -6.979913 | -8.693283 | -5.266543 | -0.5696771 | -8.083106 | 0.0000000 | 0.00e+00 | 16.3250371 | -126.23017 |
| 129350976 | 129350976 | LOC129350976 | receptor-transporting protein 3-like | NA | NA | NA | LOC129350976 | receptor-transporting protein 3-like | receptor-transporting protein 3-like.2 | 6.890013 | 5.193076 | 8.586950 | 1.7952119 | 8.056267 | 0.0000000 | 0.00e+00 | 17.9260770 | 118.60434 |
| 111584687 | 111584687 | LOC111584687 | probable E3 ubiquitin-protein ligase HERC6 | ENSAOCG00000019763 | ENSAOCG00000019763 | probable E3 ubiquitin-protein ligase HERC6 | LOC111584687_ENSAOCG00000019763 | probable E3 ubiquitin-protein ligase HERC6 | probable E3 ubiquitin-protein ligase HERC6 | 6.560506 | 5.256679 | 7.864333 | 3.1526642 | 9.983821 | 0.0000000 | 0.00e+00 | 27.4120030 | 94.38633 |
| 111574762 | 111574762 | LOC111574762 | interferon-induced GTP-binding protein Mx | ENSAOCG00000006946 | MX1 | interferon-induced GTP-binding protein Mx | LOC111574762_MX1 | interferon-induced GTP-binding protein Mx | interferon-induced GTP-binding protein Mx | 6.332014 | 5.059698 | 7.604328 | 2.9882334 | 9.874763 | 0.0000000 | 0.00e+00 | 26.8723559 | 80.56121 |
| 111562396 | 111562396 | si:dkeyp-118h9.7 | sacsin | ENSAOCG00000014036 | ENSAOCG00000014036 | sacsin-like | si:dkeyp-118h9.7_ENSAOCG00000014036 | sacsin | sacsin | 6.307530 | 5.420958 | 7.194102 | 4.7850516 | 14.116430 | 0.0000000 | 0.00e+00 | 47.4343018 | 79.20557 |
| 111565613 | 111565613 | LOC111565613 | cytochrome P450 2F2-like | ENSAOCG00000017327 | ENSAOCG00000017327 | cytochrome P450 2F2-like.6 | LOC111565613_ENSAOCG00000017327 | cytochrome P450 2F2-like | cytochrome P450 2F2-like.4 | 6.270956 | 4.887848 | 7.654063 | 2.5770157 | 8.996163 | 0.0000000 | 0.00e+00 | 22.5909561 | 77.22285 |
| 111571572 | 111571572 | LOC111571572 | up-regulator of cell proliferation-like | NA | NA | NA | LOC111571572 | up-regulator of cell proliferation-like | up-regulator of cell proliferation-like | 6.240235 | 5.361967 | 7.118504 | 4.5522962 | 14.097855 | 0.0000000 | 0.00e+00 | 47.3489032 | 75.59587 |
| entrez_ID | NCBI_symbol | NCBI_description | ensembl_ID | ensembl_symbol | ensembl_description | merged_symbol | original_merged_description | merged_description | logFC | CI.L | CI.R | AveExpr | t | P.Value | adj.P.Val | B | FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 111577915 | 111577915 | LOC111577915 | interferon alpha-inducible protein 27-like protein 2A | NA | NA | NA | LOC111577915 | interferon alpha-inducible protein 27-like protein 2A | interferon alpha-inducible protein 27-like protein 2A.2 | 6.946023 | 3.739514 | 10.1525320 | 0.7634300 | 4.298166 | 0.0000403 | 0.0001197 | 1.7857668 | 123.29948 |
| 111588695 | 111588695 | rsad2 | radical S-adenosyl methionine domain containing 2 | ENSAOCG00000009483 | rsad2 | radical S-adenosyl methionine domain containing 2 | rsad2 | radical S-adenosyl methionine domain containing 2 | radical S-adenosyl methionine domain containing 2 | 6.729393 | 3.644792 | 9.8139943 | 0.7886398 | 4.328689 | 0.0000359 | 0.0001077 | 1.8806903 | 106.10827 |
| 111568546 | 111568546 | lgals17 | galectin 17 | ENSAOCG00000023360 | ENSAOCG00000023360 | novel gene (galectin 17-like) | lgals17_ENSAOCG00000023360 | galectin 17 | galectin 17 | 6.033749 | 5.058162 | 7.0093351 | 5.3118168 | 12.271595 | 0.0000000 | 0.0000000 | 38.5335360 | 65.51479 |
| 111588557 | 111588557 | LOC111588557 | polyubiquitin-like | ENSAOCG00000014693 | ENSAOCG00000014693 | polyubiquitin-like.1 | LOC111588557_ENSAOCG00000014693 | polyubiquitin-like | polyubiquitin-like | 5.941070 | 4.447763 | 7.4343763 | 3.1584896 | 7.893963 | 0.0000000 | 0.0000000 | 17.0555197 | 61.43843 |
| 111582224 | 111582224 | si:zfos-911d5.4 | uncharacterized si:zfos-911d5.4 | NA | NA | NA | si:zfos-911d5.4 | uncharacterized si:zfos-911d5.4 | uncharacterized si:zfos-911d5.4 | 5.906808 | 2.055372 | 9.7582441 | -0.4572542 | 3.043054 | 0.0029977 | 0.0061066 | -1.7807520 | 59.99656 |
| 111576250 | 111576250 | znfx1 | zinc finger, NFX1-type containing 1 | ENSAOCG00000021079 | ZNFX1 | zinc finger NFX1-type containing 1 | znfx1 | zinc finger, NFX1-type containing 1 | zinc finger, NFX1-type containing 1 | 5.689770 | 4.087651 | 7.2918889 | 2.8292284 | 7.046597 | 0.0000000 | 0.0000000 | 13.1436990 | 51.61684 |
| 129350976 | 129350976 | LOC129350976 | receptor-transporting protein 3-like | NA | NA | NA | LOC129350976 | receptor-transporting protein 3-like | receptor-transporting protein 3-like.2 | 5.591168 | 3.887623 | 7.2947130 | 1.7952119 | 6.512211 | 0.0000000 | 0.0000000 | 10.5520428 | 48.20691 |
| 111584687 | 111584687 | LOC111584687 | probable E3 ubiquitin-protein ligase HERC6 | ENSAOCG00000019763 | ENSAOCG00000019763 | probable E3 ubiquitin-protein ligase HERC6 | LOC111584687_ENSAOCG00000019763 | probable E3 ubiquitin-protein ligase HERC6 | probable E3 ubiquitin-protein ligase HERC6 | 5.310233 | 4.002575 | 6.6178910 | 3.1526642 | 8.057475 | 0.0000000 | 0.0000000 | 17.8775960 | 39.67706 |
| 111574762 | 111574762 | LOC111574762 | interferon-induced GTP-binding protein Mx | ENSAOCG00000006946 | MX1 | interferon-induced GTP-binding protein Mx | LOC111574762_MX1 | interferon-induced GTP-binding protein Mx | interferon-induced GTP-binding protein Mx | 5.275601 | 3.999973 | 6.5512283 | 2.9882334 | 8.205924 | 0.0000000 | 0.0000000 | 18.5542392 | 38.73593 |
| 111584047 | 111584047 | usp18 | ubiquitin specific peptidase 18 | ENSAOCG00000021208 | ENSAOCG00000021208 | ubl carboxyl-terminal hydrolase 18-like | usp18_ENSAOCG00000021208 | ubiquitin specific peptidase 18 | ubiquitin specific peptidase 18 | 5.239622 | 3.081092 | 7.3981514 | 1.0352805 | 4.816388 | 0.0000053 | 0.0000188 | 3.7472913 | 37.78186 |
| 111562396 | 111562396 | si:dkeyp-118h9.7 | sacsin | ENSAOCG00000014036 | ENSAOCG00000014036 | sacsin-like | si:dkeyp-118h9.7_ENSAOCG00000014036 | sacsin | sacsin | 5.236995 | 4.349495 | 6.1244945 | 4.7850516 | 11.708290 | 0.0000000 | 0.0000000 | 35.8340920 | 37.71313 |
| 111574765 | 111574765 | LOC111574765 | interferon-induced GTP-binding protein Mx-like | ENSAOCG00000000359 | mxb | interferon-induced GTP-binding protein Mx-like | LOC111574765_mxb | interferon-induced GTP-binding protein Mx-like | interferon-induced GTP-binding protein Mx-like | 5.201757 | 3.025603 | 7.3779107 | 1.7325469 | 4.742857 | 0.0000071 | 0.0000246 | 3.5578793 | 36.80314 |
| 111589177 | 111589177 | LOC111589177 | kelch-like protein 38 | ENSAOCG00000020436 | KLHL38 | kelch-like protein 38.1 | LOC111589177_KLHL38 | kelch-like protein 38 | kelch-like protein 38.1 | 4.975737 | 2.170592 | 7.7808815 | 1.4020336 | 3.519505 | 0.0006545 | 0.0015263 | -0.4723101 | 31.46632 |
| 111588694 | 111588694 | cmpk2 | cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial | ENSAOCG00000000586 | CMPK2 | cytidine/uridine monophosphate kinase 2 | cmpk2 | cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial | cytidine monophosphate (UMP-CMP) kinase 2, mitochondrial | 4.972745 | 3.647360 | 6.2981308 | 1.8164046 | 7.444466 | 0.0000000 | 0.0000000 | 14.7524318 | 31.40115 |
| 111565606 | 111565606 | LOC111565606 | C-C motif chemokine 21-like | ENSAOCG00000021849 | ENSAOCG00000021849 | C-C motif chemokine 21-like | LOC111565606_ENSAOCG00000021849 | C-C motif chemokine 21-like | C-C motif chemokine 21-like | 4.963170 | 3.768096 | 6.1582434 | 3.9229597 | 8.240318 | 0.0000000 | 0.0000000 | 18.8359784 | 31.19342 |
| 129349373 | 129349373 | LOC129349373 | probable serpin E3 | NA | NA | NA | LOC129349373 | probable serpin E3 | probable serpin E3.21 | 4.899351 | 1.841616 | 7.9570865 | 0.4723930 | 3.179203 | 0.0019705 | 0.0041719 | -1.3995279 | 29.84363 |
| 111568689 | 111568689 | LOC111568689 | insulin-like growth factor-binding protein 1 | ENSAOCG00000018285 | igfbp1b | insulin-like growth factor-binding protein 1.1 | LOC111568689_igfbp1b | insulin-like growth factor-binding protein 1 | insulin-like growth factor-binding protein 1 | 4.895474 | 2.459775 | 7.3311734 | 3.0783777 | 3.987958 | 0.0001276 | 0.0003430 | 0.9459554 | 29.76354 |
| 111583825 | 111583825 | LOC111583825 | C-reactive protein-like | ENSAOCG00000004271 | ENSAOCG00000004271 | pentraxin fusion protein-like | LOC111583825_ENSAOCG00000004271 | C-reactive protein-like | C-reactive protein-like.2 | -4.886181 | -9.547930 | -0.2244321 | 1.5816666 | -2.079697 | 0.0401325 | 0.0628315 | -3.9459846 | -29.57243 |
| 111571474 | 111571474 | il4i1 | interleukin 4 induced 1 | ENSAOCG00000023672 | ENSAOCG00000023672 | L-amino-acid oxidase-like.2 | il4i1_ENSAOCG00000023672 | interleukin 4 induced 1 | interleukin 4 induced 1 | 4.824605 | 2.853447 | 6.7957633 | 1.9138440 | 4.856459 | 0.0000045 | 0.0000162 | 3.9529800 | 28.33680 |
| 111586659 | 111586659 | LOC111586659 | probable E3 ubiquitin-protein ligase HERC3 | NA | NA | NA | LOC111586659 | probable E3 ubiquitin-protein ligase HERC3 | probable E3 ubiquitin-protein ligase HERC3 | 4.688654 | 3.538006 | 5.8393015 | 2.7457832 | 8.085096 | 0.0000000 | 0.0000000 | 17.9764108 | 25.78846 |
NULL
Attenuation plot
Alluvial plot
| entrez_ID | ensembl_ID_CPFT3IOP | merged_symbol_CPFT3IOP | merged_description_CPFT3IOP | logFC_CPFT3IOP | logFC_CPF | FC_CPFT3IOP | FC_CPF | rank | |
|---|---|---|---|---|---|---|---|---|---|
| 9269 | 111574513 | NA | LOC111574513 | complement C1q-like protein 4.1 | -1.508325 | 2.088413 | -2.844797 | 4.252800 | 3 |
| 16109 | 111583609 | ENSAOCG00000010276 | LOC111583609_ENSAOCG00000010276 | collagenase 3 | -3.501439 | 1.194282 | -11.324999 | 2.288309 | 4 |
| 7372 | 111572094 | NA | LOC111572094 | 2-epi-5-epi-valiolone synthase-like | -1.213500 | 1.199997 | -2.318996 | 2.297392 | 6 |
| 12086 | 111578169 | ENSAOCG00000008659 | fgfbp2a | fibroblast growth factor binding protein 2a | -1.310079 | 1.073588 | -2.479551 | 2.104661 | 7 |
| entrez_ID | ensembl_ID_CPFT3IOP | merged_symbol_CPFT3IOP | merged_description_CPFT3IOP | logFC_CPFT3IOP | logFC_CPF | FC_CPFT3IOP | FC_CPF | rank | |
|---|---|---|---|---|---|---|---|---|---|
| 8195 | 111573140 | ENSAOCG00000004145 | LOC111573140_steap4 | metalloreductase STEAP4-like | 2.912831 | -3.356776 | 7.530948 | -10.244485 | 4 |
| 7852 | 111572709 | ENSAOCG00000000604 | LOC111572709_PTCHD3 | patched domain-containing protein 3-like | 3.438335 | -1.797154 | 10.840320 | -3.475339 | 7 |
| 13760 | 111580318 | NA | LOC111580318 | UDP-glucuronosyltransferase 2A1-like.6 | 2.734377 | -1.949602 | 6.654713 | -3.862681 | 9 |
| 14285 | 111581053 | ENSAOCG00000014793 | LOC111581053_ENSAOCG00000014793 | proproteinase E-like | 2.294088 | -2.273990 | 4.904437 | -4.836590 | 10 |
| 7108 | 111571739 | ENSAOCG00000017399 | LOC111571739_ENSAOCG00000017399 | complement C1q-like protein 2 | 1.964056 | -2.209516 | 3.901574 | -4.625199 | 12 |
| 8199 | 111573147 | ENSAOCG00000004133 | LOC111573147_ENSAOCG00000004133 | serum amyloid P-component-like.1 | 2.576138 | -1.440352 | 5.963411 | -2.713870 | 14 |
| 15270 | 111582409 | ENSAOCG00000010775 | aqp8a.2_ENSAOCG00000010775 | aquaporin 8a, tandem duplicate 2 | 1.323795 | -2.582604 | 2.503237 | -5.990200 | 15 |
| 9181 | 111574400 | ENSAOCG00000020520 | LOC111574400_ENSAOCG00000020520 | WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2-like | 3.280654 | -1.171148 | 9.717962 | -2.251908 | 18 |
| 2714 | 111565970 | ENSAOCG00000009607 | LOC111565970_CSTA | cystatin-B-like.1 | 1.649649 | -1.369124 | 3.137573 | -2.583136 | 20 |
| 20342 | 129347240 | NA | LOC129347240 | glutathione S-transferase A-like.13 | 2.610210 | -1.180202 | 6.105927 | -2.266085 | 20 |
| 5263 | 111569306 | ENSAOCG00000021939 | LOC111569306_rdh12l | retinol dehydrogenase 12-like | 1.731422 | -1.239799 | 3.320549 | -2.361656 | 21 |
| 19825 | 118469194 | NA | LOC118469194 | IgGFc-binding protein-like | 1.130180 | -1.455974 | 2.188860 | -2.743416 | 25 |
| 7636 | 111572425 | NA | LOC111572425 | UDP-glucuronosyltransferase 2A1-like.2 | 1.133238 | -1.371671 | 2.193505 | -2.587701 | 26 |
| 20010 | 118470365 | NA | LOC118470365 | uncharacterized LOC118470365 | 1.214013 | -1.194063 | 2.319821 | -2.287961 | 29 |
| 2542 | 111565748 | ENSAOCG00000016673 | c1h15orf48_zgc:153317 | chromosome 1 C15orf48 homolog | 1.532034 | -1.051117 | 2.891933 | -2.072133 | 30 |
| 10498 | 111576134 | ENSAOCG00000024487 | LOC111576134_gstr | glutathione S-transferase A-like.11 | 1.042040 | -1.359144 | 2.059137 | -2.565329 | 31 |
| 15205 | 111582297 | ENSAOCG00000014922 | LOC111582297_ENSAOCG00000014922 | cytochrome P450 2F2-like.14 | 1.076125 | -1.224476 | 2.108366 | -2.336705 | 32 |
| 18779 | 111587842 | ENSAOCG00000020073 | LOC111587842_ENSAOCG00000020073 | cytochrome c oxidase subunit 6A, mitochondrial.1 | 1.286129 | -1.056158 | 2.438728 | -2.079387 | 32 |
| 10616 | 111576278 | ENSAOCG00000019724 | samhd1 | SAM domain and HD domain 1 | 1.398650 | -1.050244 | 2.636547 | -2.070880 | 32 |
| 11193 | 111577049 | ENSAOCG00000007922 | LOC111577049_prss1 | trypsin-3-like.1 | 1.184164 | -1.135683 | 2.272317 | -2.197226 | 33 |
[1] "0 differentially expressed genes upregulated by both CPF and T3IOP"
[1] "0 differentially expressed genes downregulated by both CPF and T3IOP"
[1] "4 differentially expressed genes downregulated by T3IOP but upregulated by CPF"
[1] "20 differentially expressed genes upregulated by T3IOP but downreegulated by CPF"
Error: object 'T3IOP_only' not found
| entrez_ID | NCBI_symbol | NCBI_description | ensembl_ID | ensembl_symbol | ensembl_description | merged_symbol | original_merged_description | merged_description | logFC | CI.L | CI.R | AveExpr | t | P.Value | adj.P.Val | B | FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 129348303 | 129348303 | LOC129348303 | uncharacterized LOC129348303 | NA | NA | NA | LOC129348303 | uncharacterized LOC129348303 | uncharacterized LOC129348303 | -10.068848 | -13.977676 | -6.160020 | 3.1991964 | -5.111081 | 0.0000016 | 7.20e-06 | 4.9057973 | -1074.05197 |
| 118470957 | 118470957 | LOC118470957 | uncharacterized LOC118470957 | NA | NA | NA | LOC118470957 | uncharacterized LOC118470957 | uncharacterized LOC118470957 | -9.506054 | -14.438282 | -4.573826 | 1.5594816 | -3.824165 | 0.0002294 | 6.81e-04 | 0.4087158 | -727.12211 |
| 111588695 | 111588695 | rsad2 | radical S-adenosyl methionine domain containing 2 | ENSAOCG00000009483 | rsad2 | radical S-adenosyl methionine domain containing 2 | rsad2 | radical S-adenosyl methionine domain containing 2 | radical S-adenosyl methionine domain containing 2 | 8.754387 | 5.680109 | 11.828665 | 0.7886398 | 5.650177 | 0.0000002 | 9.00e-07 | 7.0320258 | 431.85001 |
| 111577915 | 111577915 | LOC111577915 | interferon alpha-inducible protein 27-like protein 2A | NA | NA | NA | LOC111577915 | interferon alpha-inducible protein 27-like protein 2A | interferon alpha-inducible protein 27-like protein 2A.2 | 8.528721 | 5.330104 | 11.727338 | 0.7634300 | 5.290554 | 0.0000007 | 3.60e-06 | 5.6193709 | 369.31839 |
| 111588653 | 111588653 | LOC111588653 | calpain-1 catalytic subunit-like | NA | NA | NA | LOC111588653 | calpain-1 catalytic subunit-like | calpain-1 catalytic subunit-like.5 | -8.430433 | -10.463852 | -6.397014 | 3.1497123 | -8.226262 | 0.0000000 | 0.00e+00 | 18.2424731 | -344.99535 |
| 111565606 | 111565606 | LOC111565606 | C-C motif chemokine 21-like | ENSAOCG00000021849 | ENSAOCG00000021849 | C-C motif chemokine 21-like | LOC111565606_ENSAOCG00000021849 | C-C motif chemokine 21-like | C-C motif chemokine 21-like | 7.655180 | 6.465892 | 8.844468 | 3.9229597 | 12.771674 | 0.0000000 | 0.00e+00 | 40.9585606 | 201.57603 |
| 111564448 | 111564448 | LOC111564448 | acidic mammalian chitinase-like | ENSAOCG00000003252 | ENSAOCG00000003252 | CHIO1, chitinase O-1, chia2/9-like | LOC111564448_ENSAOCG00000003252 | acidic mammalian chitinase-like | acidic mammalian chitinase-like.1 | -7.495890 | -8.258235 | -6.733545 | 5.1246678 | -19.509732 | 0.0000000 | 0.00e+00 | 69.4069184 | -180.50438 |
| 111568546 | 111568546 | lgals17 | galectin 17 | ENSAOCG00000023360 | ENSAOCG00000023360 | novel gene (galectin 17-like) | lgals17_ENSAOCG00000023360 | galectin 17 | galectin 17 | 7.418167 | 6.441187 | 8.395147 | 5.3118168 | 15.065744 | 0.0000000 | 0.00e+00 | 51.8013770 | 171.03729 |
| 111576250 | 111576250 | znfx1 | zinc finger, NFX1-type containing 1 | ENSAOCG00000021079 | ZNFX1 | zinc finger NFX1-type containing 1 | znfx1 | zinc finger, NFX1-type containing 1 | zinc finger, NFX1-type containing 1 | 7.309194 | 5.711657 | 8.906730 | 2.8292284 | 9.078167 | 0.0000000 | 0.00e+00 | 22.9508086 | 158.59392 |
| 111571474 | 111571474 | il4i1 | interleukin 4 induced 1 | ENSAOCG00000023672 | ENSAOCG00000023672 | L-amino-acid oxidase-like.2 | il4i1_ENSAOCG00000023672 | interleukin 4 induced 1 | interleukin 4 induced 1 | 7.246212 | 5.296486 | 9.195938 | 1.9138440 | 7.374234 | 0.0000000 | 0.00e+00 | 14.7323110 | 151.81936 |
| 111576689 | 111576689 | LOC111576689 | protein translocase subunit SecA-like | NA | NA | NA | LOC111576689 | protein translocase subunit SecA-like | protein translocase subunit SecA-like | 7.245204 | 4.470180 | 10.020229 | -1.0328861 | 5.180400 | 0.0000012 | 5.50e-06 | 5.0171681 | 151.71337 |
| 111588557 | 111588557 | LOC111588557 | polyubiquitin-like | ENSAOCG00000014693 | ENSAOCG00000014693 | polyubiquitin-like.1 | LOC111588557_ENSAOCG00000014693 | polyubiquitin-like | polyubiquitin-like | 7.185437 | 5.695307 | 8.675567 | 3.1584896 | 9.567721 | 0.0000000 | 0.00e+00 | 25.3551057 | 145.55668 |
| 118469095 | 118469095 | sb:cb1081 | sterile alpha motif domain-containing protein 9-like | NA | NA | NA | sb:cb1081 | sterile alpha motif domain-containing protein 9-like | sterile alpha motif domain-containing protein 9-like.3 | 7.184799 | 6.098363 | 8.271235 | 4.2081541 | 13.121694 | 0.0000000 | 0.00e+00 | 42.7175548 | 145.49229 |
| 111573059 | 111573059 | LOC111573059 | tyrosinase-like | NA | NA | NA | LOC111573059 | tyrosinase-like | tyrosinase-like.1 | -6.979913 | -8.693283 | -5.266543 | -0.5696771 | -8.083106 | 0.0000000 | 0.00e+00 | 16.3250371 | -126.23017 |
| 129350976 | 129350976 | LOC129350976 | receptor-transporting protein 3-like | NA | NA | NA | LOC129350976 | receptor-transporting protein 3-like | receptor-transporting protein 3-like.2 | 6.890013 | 5.193076 | 8.586950 | 1.7952119 | 8.056267 | 0.0000000 | 0.00e+00 | 17.9260770 | 118.60434 |
| 111584687 | 111584687 | LOC111584687 | probable E3 ubiquitin-protein ligase HERC6 | ENSAOCG00000019763 | ENSAOCG00000019763 | probable E3 ubiquitin-protein ligase HERC6 | LOC111584687_ENSAOCG00000019763 | probable E3 ubiquitin-protein ligase HERC6 | probable E3 ubiquitin-protein ligase HERC6 | 6.560506 | 5.256679 | 7.864333 | 3.1526642 | 9.983821 | 0.0000000 | 0.00e+00 | 27.4120030 | 94.38633 |
| 111574762 | 111574762 | LOC111574762 | interferon-induced GTP-binding protein Mx | ENSAOCG00000006946 | MX1 | interferon-induced GTP-binding protein Mx | LOC111574762_MX1 | interferon-induced GTP-binding protein Mx | interferon-induced GTP-binding protein Mx | 6.332014 | 5.059698 | 7.604328 | 2.9882334 | 9.874763 | 0.0000000 | 0.00e+00 | 26.8723559 | 80.56121 |
| 111562396 | 111562396 | si:dkeyp-118h9.7 | sacsin | ENSAOCG00000014036 | ENSAOCG00000014036 | sacsin-like | si:dkeyp-118h9.7_ENSAOCG00000014036 | sacsin | sacsin | 6.307530 | 5.420958 | 7.194102 | 4.7850516 | 14.116430 | 0.0000000 | 0.00e+00 | 47.4343018 | 79.20557 |
| 111565613 | 111565613 | LOC111565613 | cytochrome P450 2F2-like | ENSAOCG00000017327 | ENSAOCG00000017327 | cytochrome P450 2F2-like.6 | LOC111565613_ENSAOCG00000017327 | cytochrome P450 2F2-like | cytochrome P450 2F2-like.4 | 6.270956 | 4.887848 | 7.654063 | 2.5770157 | 8.996163 | 0.0000000 | 0.00e+00 | 22.5909561 | 77.22285 |
| 111571572 | 111571572 | LOC111571572 | up-regulator of cell proliferation-like | NA | NA | NA | LOC111571572 | up-regulator of cell proliferation-like | up-regulator of cell proliferation-like | 6.240235 | 5.361967 | 7.118504 | 4.5522962 | 14.097855 | 0.0000000 | 0.00e+00 | 47.3489032 | 75.59587 |
| entrez_ID | NCBI_symbol | NCBI_description | ensembl_ID | ensembl_symbol | ensembl_description | merged_symbol | original_merged_description | merged_description | logFC | CI.L | CI.R | AveExpr | t | P.Value | adj.P.Val | B | FC | |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 129348303 | 129348303 | LOC129348303 | uncharacterized LOC129348303 | NA | NA | NA | LOC129348303 | uncharacterized LOC129348303 | uncharacterized LOC129348303 | -9.732320 | -13.418829 | -6.045812 | 3.1991964 | -5.238183 | 0.0000009 | 0.0000070 | 5.4255579 | -850.59009 |
| 118470957 | 118470957 | LOC118470957 | uncharacterized LOC118470957 | NA | NA | NA | LOC118470957 | uncharacterized LOC118470957 | uncharacterized LOC118470957 | -8.994404 | -13.585266 | -4.403540 | 1.5594816 | -3.887385 | 0.0001832 | 0.0007483 | 0.6272601 | -510.01768 |
| 111588653 | 111588653 | LOC111588653 | calpain-1 catalytic subunit-like | NA | NA | NA | LOC111588653 | calpain-1 catalytic subunit-like | calpain-1 catalytic subunit-like.5 | -8.061279 | -9.976454 | -6.146103 | 3.1497123 | -8.351700 | 0.0000000 | 0.0000000 | 18.9542624 | -267.10790 |
| 111573059 | 111573059 | LOC111573059 | tyrosinase-like | NA | NA | NA | LOC111573059 | tyrosinase-like | tyrosinase-like.1 | -6.709533 | -8.422903 | -4.996163 | -0.5696771 | -7.769991 | 0.0000000 | 0.0000000 | 15.0572505 | -104.65758 |
| 111564448 | 111564448 | LOC111564448 | acidic mammalian chitinase-like | ENSAOCG00000003252 | ENSAOCG00000003252 | CHIO1, chitinase O-1, chia2/9-like | LOC111564448_ENSAOCG00000003252 | acidic mammalian chitinase-like | acidic mammalian chitinase-like.1 | -5.743945 | -6.231172 | -5.256718 | 5.1246678 | -23.391534 | 0.0000000 | 0.0000000 | 85.0518517 | -53.59197 |
| 111582289 | 111582289 | LOC111582289 | hatching enzyme 1.2-like | NA | NA | NA | LOC111582289 | hatching enzyme 1.2-like | hatching enzyme 1.2-like | -5.029215 | -6.119961 | -3.938469 | 0.5268815 | -9.148632 | 0.0000000 | 0.0000000 | 21.9421432 | -32.65462 |
| 111586982 | 111586982 | LOC111586982 | alpha-1-antitrypsin homolog | ENSAOCG00000011906 | ENSAOCG00000011906 | alpha-1-antitrypsin homolog.1 | LOC111586982_ENSAOCG00000011906 | alpha-1-antitrypsin homolog | alpha-1-antitrypsin homolog.2 | 4.976365 | 3.631521 | 6.321209 | 0.8618981 | 7.342091 | 0.0000000 | 0.0000000 | 14.6435494 | 31.48003 |
| 111562991 | 111562991 | aqp10a | aquaporin 10a | ENSAOCG00000008773 | aqp10a | aquaporin-10-like | aqp10a | aquaporin 10a | aquaporin 10a | 4.781471 | 3.751631 | 5.811312 | 0.4504553 | 9.212365 | 0.0000000 | 0.0000000 | 22.7693300 | 27.50213 |
| 118470600 | 118470600 | LOC118470600 | uncharacterized LOC118470600 | NA | NA | NA | LOC118470600 | uncharacterized LOC118470600 | uncharacterized LOC118470600 | 4.680772 | 4.049469 | 5.312075 | -0.1871561 | 14.711577 | 0.0000000 | 0.0000000 | 47.7876207 | 25.64796 |
| 111582738 | 111582738 | LOC111582738 | nuclear factor interleukin-3-regulated protein-like | ENSAOCG00000021476 | ENSAOCG00000021476 | nuclear factor interleukin-3-regulated protein-like.1 | LOC111582738_ENSAOCG00000021476 | nuclear factor interleukin-3-regulated protein-like | nuclear factor interleukin-3-regulated protein-like | 4.623166 | 4.162032 | 5.084301 | 2.5774259 | 19.892603 | 0.0000000 | 0.0000000 | 71.8017252 | 24.64403 |
| 118469143 | 118469143 | LOC118469143 | uncharacterized LOC118469143 | NA | NA | NA | LOC118469143 | uncharacterized LOC118469143 | uncharacterized LOC118469143 | -4.510040 | -5.157803 | -3.862277 | 2.8303418 | -13.814768 | 0.0000000 | 0.0000000 | 44.9684962 | -22.78543 |
| 111579324 | 111579324 | LOC111579324 | lactase/phlorizin hydrolase-like | ENSAOCG00000014483 | LCT | lactase-phlorizin hydrolase-like.1 | LOC111579324_LCT | lactase/phlorizin hydrolase-like | lactase/phlorizin hydrolase-like | 4.379545 | 3.820212 | 4.938879 | 4.5659675 | 15.535939 | 0.0000000 | 0.0000000 | 53.9126034 | 20.81491 |
| 111574400 | 111574400 | LOC111574400 | WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2-like | ENSAOCG00000020520 | ENSAOCG00000020520 | WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2-like | LOC111574400_ENSAOCG00000020520 | WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2-like | WAP, Kazal, immunoglobulin, Kunitz and NTR domain-containing protein 2-like | 4.331794 | 4.066081 | 4.597506 | 3.4290414 | 32.347131 | 0.0000000 | 0.0000000 | 112.4193036 | 20.13723 |
| 118471637 | 118471637 | LOC118471637 | uncharacterized LOC118471637 | NA | NA | NA | LOC118471637 | uncharacterized LOC118471637 | uncharacterized LOC118471637 | -4.181974 | -4.888625 | -3.475323 | 5.2649032 | -11.742369 | 0.0000000 | 0.0000000 | 36.0408087 | -18.15096 |
| 111565613 | 111565613 | LOC111565613 | cytochrome P450 2F2-like | ENSAOCG00000017327 | ENSAOCG00000017327 | cytochrome P450 2F2-like.6 | LOC111565613_ENSAOCG00000017327 | cytochrome P450 2F2-like | cytochrome P450 2F2-like.4 | 4.158361 | 2.760076 | 5.556646 | 2.5770157 | 5.900733 | 0.0000001 | 0.0000005 | 8.0679960 | 17.85630 |
| 111566579 | 111566579 | LOC111566579 | placenta-specific gene 8 protein-like | ENSAOCG00000010064 | plac8.2 | placenta-specific gene 8 protein-like.1 | LOC111566579_plac8.2 | placenta-specific gene 8 protein-like | placenta-specific gene 8 protein-like | 3.957414 | 2.940895 | 4.973933 | 0.3953221 | 7.724593 | 0.0000000 | 0.0000000 | 16.1030459 | 15.53461 |
| 111586185 | 111586185 | dio3a | iodothyronine deiodinase 3a | NA | NA | NA | dio3a | iodothyronine deiodinase 3a | iodothyronine deiodinase 3a | 3.909003 | 3.607792 | 4.210213 | 2.7162596 | 25.749855 | 0.0000000 | 0.0000000 | 92.2645967 | 15.02197 |
| 111564199 | 111564199 | LOC111564199 | meprin A subunit beta-like | NA | NA | NA | LOC111564199 | meprin A subunit beta-like | meprin A subunit beta-like | -3.837511 | -6.366941 | -1.308081 | -0.6712350 | -3.010278 | 0.0033101 | 0.0092976 | -1.8205550 | -14.29572 |
| 111574814 | 111574814 | LOC111574814 | hemoglobin subunit beta-like | ENSAOCG00000004104 | HBE1 | hemoglobin subunit beta-1, MN-cluster | LOC111574814_HBE1 | hemoglobin subunit beta-like | hemoglobin subunit beta-like.2 | -3.747877 | -4.141205 | -3.354549 | 5.9702150 | -18.906457 | 0.0000000 | 0.0000000 | 68.4349934 | -13.43456 |
| 111570504 | 111570504 | cdh27 | cadherin 27 | ENSAOCG00000012441 | ENSAOCG00000012441 | cadherin-like protein 26.1 | cdh27_ENSAOCG00000012441 | cadherin 27 | cadherin 27 | -3.727387 | -4.401882 | -3.052893 | 1.0268691 | -10.964920 | 0.0000000 | 0.0000000 | 31.1827063 | -13.24510 |
Attenuation plot
Alluvial plot
Venn diagrams
R version 4.3.2 (2023-10-31 ucrt)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows 11 x64 (build 22631)
Matrix products: default
locale:
[1] LC_COLLATE=English_United States.utf8 LC_CTYPE=English_United States.utf8
[3] LC_MONETARY=English_United States.utf8 LC_NUMERIC=C
[5] LC_TIME=English_United States.utf8
time zone: Asia/Shanghai
tzcode source: internal
attached base packages:
[1] grid stats4 stats graphics grDevices utils datasets methods
[9] base
other attached packages:
[1] venneuler_1.1-4 rJava_1.0-11 ggalluvial_0.12.5
[4] mgsa_1.50.0 gplots_3.1.3 aplot_0.2.2
[7] patchwork_1.2.0 enrichplot_1.22.0 clusterProfiler_4.10.0
[10] biomaRt_2.58.2 ggVennDiagram_1.5.2 ggpubr_0.6.0
[13] cowplot_1.1.3 factoextra_1.0.7 ggalt_0.4.0
[16] ggrepel_0.9.5 dendextend_1.17.1 GetoptLong_1.0.5
[19] ComplexHeatmap_2.18.0 knitr_1.45 kneedle_1.0.0
[22] gridBase_0.4-7 RColorBrewer_1.1-3 DESeq2_1.42.0
[25] SummarizedExperiment_1.32.0 MatrixGenerics_1.14.0 matrixStats_1.2.0
[28] gridExtra_2.3 ggforce_0.4.1 lubridate_1.9.3
[31] forcats_1.0.0 stringr_1.5.1 dplyr_1.1.4
[34] purrr_1.0.2 readr_2.1.5 tidyr_1.3.1
[37] tibble_3.2.1 ggplot2_3.5.0 tidyverse_2.0.0
[40] magrittr_2.0.3 edgeR_4.0.14 limma_3.58.1
[43] tximport_1.30.0 GenomicFeatures_1.54.1 AnnotationDbi_1.64.1
[46] Biobase_2.62.0 formattable_0.2.1 jsonlite_1.8.8
[49] BSgenome_1.70.2 rtracklayer_1.62.0 BiocIO_1.12.0
[52] Biostrings_2.70.2 XVector_0.42.0 GenomicRanges_1.54.1
[55] GenomeInfoDb_1.38.5 IRanges_2.36.0 S4Vectors_0.40.2
[58] BiocGenerics_0.48.1
loaded via a namespace (and not attached):
[1] vroom_1.6.5 progress_1.2.3
[3] urlchecker_1.0.1 vctrs_0.6.5
[5] digest_0.6.34 png_0.1-8
[7] shape_1.4.6.1 proxy_0.4-27
[9] magick_2.8.2 MASS_7.3-60
[11] reshape2_1.4.4 httpuv_1.6.14
[13] foreach_1.5.2 qvalue_2.34.0
[15] withr_3.0.0 xfun_0.41
[17] ggfun_0.1.4 ellipsis_0.3.2
[19] memoise_2.0.1 commonmark_1.9.1
[21] gson_0.1.0 profvis_0.3.8
[23] tidytree_0.4.6 zoo_1.8-12
[25] GlobalOptions_0.1.2 gtools_3.9.5
[27] quantmod_0.4.26 prettyunits_1.2.0
[29] KEGGREST_1.42.0 promises_1.2.1
[31] httr_1.4.7 rstatix_0.7.2
[33] restfulr_0.0.15 rstudioapi_0.16.0
[35] units_0.8-5 miniUI_0.1.1.1
[37] generics_0.1.3 DOSE_3.28.2
[39] curl_5.2.0 zlibbioc_1.48.0
[41] Rsubread_2.16.1 ggraph_2.1.0
[43] polyclip_1.10-6 GenomeInfoDbData_1.2.11
[45] SparseArray_1.2.3 interactiveDisplayBase_1.40.0
[47] xtable_1.8-4 doParallel_1.0.17
[49] evaluate_0.23 S4Arrays_1.2.0
[51] BiocFileCache_2.10.2 hms_1.1.3
[53] colorspace_2.1-0 filelock_1.0.3
[55] later_1.3.2 viridis_0.6.5
[57] ggtree_3.10.1 lattice_0.21-9
[59] XML_3.99-0.16.1 shadowtext_0.1.3
[61] xts_0.13.2 ggupset_0.3.0
[63] class_7.3-22 pillar_1.9.0
[65] nlme_3.1-163 iterators_1.0.14
[67] caTools_1.18.2 compiler_4.3.2
[69] stringi_1.8.3 sf_1.0-16
[71] devtools_2.4.5 GenomicAlignments_1.38.2
[73] plyr_1.8.9 crayon_1.5.2
[75] abind_1.4-5 gridGraphics_0.5-1
[77] ggtext_0.1.2 locfit_1.5-9.8
[79] graphlayouts_1.1.0 bit_4.0.5
[81] fastmatch_1.1-4 codetools_0.2-19
[83] TTR_0.24.4 bslib_0.7.0
[85] e1071_1.7-14 mime_0.12
[87] splines_4.3.2 markdown_1.12
[89] circlize_0.4.16 Rcpp_1.0.12
[91] dbplyr_2.5.0 HDO.db_0.99.1
[93] Rttf2pt1_1.3.12 gridtext_0.1.5
[95] blob_1.2.4 utf8_1.2.4
[97] clue_0.3-65 BiocVersion_3.18.1
[99] fs_1.6.3 pkgbuild_1.4.4
[101] ggsignif_0.6.4 ggplotify_0.1.2
[103] Matrix_1.6-5 statmod_1.5.0
[105] tzdb_0.4.0 tweenr_2.0.2
[107] pkgconfig_2.0.3 tools_4.3.2
[109] cachem_1.0.8 RSQLite_2.3.5
[111] viridisLite_0.4.2 DBI_1.2.2
[113] fastmap_1.1.1 rmarkdown_2.26
[115] scales_1.3.0 usethis_2.2.3
[117] Rsamtools_2.18.0 broom_1.0.5
[119] AnnotationHub_3.10.0 sass_0.4.9
[121] BiocManager_1.30.22 carData_3.0-5
[123] snow_0.4-4 farver_2.1.1
[125] tidygraph_1.3.1 scatterpie_0.2.2
[127] yaml_2.3.8 cli_3.6.2
[129] lifecycle_1.0.4 sessioninfo_1.2.2
[131] backports_1.4.1 BiocParallel_1.36.0
[133] timechange_0.3.0 gtable_0.3.4
[135] rjson_0.2.21 parallel_4.3.2
[137] ape_5.7-1 bitops_1.0-7
[139] bit64_4.0.5 assertthat_0.2.1
[141] yulab.utils_0.1.4 jquerylib_0.1.4
[143] GOSemSim_2.28.1 lazyeval_0.2.2
[145] shiny_1.8.1.1 htmltools_0.5.8.1
[147] proj4_1.0-14 GO.db_3.18.0
[149] rappdirs_0.3.3 glue_1.7.0
[151] RCurl_1.98-1.14 treeio_1.26.0
[153] classInt_0.4-10 igraph_2.0.1.1
[155] extrafontdb_1.0 R6_2.5.1
[157] dupRadar_1.32.0 labeling_0.4.3
[159] cluster_2.1.4 pkgload_1.3.4
[161] DelayedArray_0.28.0 tidyselect_1.2.1
[163] maps_3.4.2 xml2_1.3.6
[165] ash_1.0-15 car_3.1-2
[167] emo_0.0.0.9000 munsell_0.5.1
[169] KernSmooth_2.23-22 data.table_1.15.0
[171] htmlwidgets_1.6.4 fgsea_1.28.0
[173] rlang_1.1.3 extrafont_0.19
[175] remotes_2.5.0 ggnewscale_0.4.9
[177] fansi_1.0.6 Cairo_1.6-2
Analysis Notebook
Reynaud, Vianello, et
al. “The multi-level effect of chlorpyrifos during clownfish
metamorphosis”
RNotebook by Stefano Vianello,
Marine Eco-Evo-Devo unit, Academia Sinica Marine Research Station
This work is licensed under a
Creative
Commons Attribution-NonCommercial 4.0 International License with the
additional reservation of the rights to non-human text and data mining,
AI training, and similar technologies, which are not granted.